2016–17 UEFA Europa League qualifying phase and play-off round

The schedule of the competition was as follows (all draws were held at the UEFA headquarters in Nyon, Switzerland, unless stated otherwise).{{cite web |title=2016/17 Europa League match calendar |url=http://www.uefa.com/uefaeuropaleague/season=2017/competitionformat/index.html |archive-url=https://web.archive.org/web/20160324023720/http://www.uefa.com/uefaeuropaleague/season=2017/competitionformat/index.html |url-status=dead |archive-date=March 24, 2016 |website=UEFA |publisher=Union of European Football Associations |access-date=12 June 2016}}{{cite web |url=https://kassiesa.net/uefa/calendar2016.html |title=UEFA European Football Calendar 2016/2017 |publisher=Bert Kassies |url-status=dead |archive-url=https://web.archive.org/web/20160701101829/http://kassiesa.home.xs4all.nl/bert/uefa/calendar2016.html |archive-date=2016-07-01 }}

class="wikitable" style="text-align:center"
Round !Draw date and time !First leg !Second leg
First qualifying round |20 June 2016, 13:00{{cite web |title=UEFA Europa League first qualifying round draw |url=https://www.uefa.com/uefaeuropaleague/draws/2017/2000788/ |website=UEFA |publisher=Union of European Football Associations |access-date=12 June 2016}}{{cite web |title=Watch the Europa League draws on Monday |url=http://www.uefa.com/uefaeuropaleague/news/newsid=2379000.html |archive-url=https://web.archive.org/web/20160619050444/http://www.uefa.com/uefaeuropaleague/news/newsid=2379000.html |url-status=dead |archive-date=June 19, 2016 |website=UEFA |publisher=Union of European Football Associations |date=17 June 2016 |access-date=19 June 2016}} |30 June 2016 |7 July 2016
Second qualifying round |20 June 2016, 14:30{{cite web |title=UEFA Europa League second qualifying round draw |url=https://www.uefa.com/uefaeuropaleague/draws/2017/2000788/ |website=UEFA |publisher=Union of European Football Associations |access-date=12 June 2016}} |14 July 2016 |21 July 2016
Third qualifying round |15 July 2016, 13:00{{cite web |title=UEFA Europa League third qualifying round draw |url=https://www.uefa.com/uefaeuropaleague/draws/2017/2000790/ |website=UEFA |publisher=Union of European Football Associations |access-date=12 June 2016}}{{cite web |title=Europa League third qualifying round draw: Friday |url=http://www.uefa.com/uefaeuropaleague/news/newsid=2390237.html |archive-url=https://web.archive.org/web/20160713163654/http://www.uefa.com/uefaeuropaleague/news/newsid=2390237.html |url-status=dead |archive-date=July 13, 2016 |website=UEFA |publisher=Union of European Football Associations |date=11 July 2016 |access-date=14 July 2016}} |28 July 2016 |4 August 2016
Play-off round |5 August 2016, 13:00{{cite web |title=UEFA Europa League play-off draw |url=https://www.uefa.com/uefaeuropaleague/draws/2017/2000791/ |website=UEFA |publisher=Union of European Football Associations |access-date=12 June 2016}}{{cite web |title=UEFA Europa League play-off draw live: seedings |url=http://www.uefa.com/uefaeuropaleague/news/newsid=2394114.html |archive-url=https://archive.today/20160818211820/http://www.uefa.com/uefaeuropaleague/news/newsid=2394114.html |url-status=dead |archive-date=August 18, 2016 |website=UEFA |publisher=Union of European Football Associations |date=4 August 2016 |access-date=5 August 2016}} |18 August 2016 |25 August 2016

Matches could also be played on Tuesdays or Wednesdays instead of the regular Thursdays due to scheduling conflicts.

In the qualifying phase and play-off round, each tie was played over two legs, with each team playing one leg at home. The team that scored more goals on aggregate over the two legs advanced to the next round. If the aggregate score was level, the away goals rule would be applied, i.e., the team that scored more goals away from home over the two legs advanced. If away goals were also equal, then thirty minutes of extra time would be played, divided into two fifteen-minutes halves. The away goals rule would be again applied after extra time, i.e., if there were goals scored during extra time and the aggregate score was still level, the visiting team advanced by virtue of more away goals scored. If no goals were scored during extra time, the tie would be decided by penalty shoot-out.

In the draws for each round, teams were seeded based on their UEFA club coefficients at the beginning of the season, with the teams divided into seeded and unseeded pots. A seeded team was drawn against an unseeded team, with the order of legs in each tie decided by draw. Due to the limited time between matches, the draws for the second and third qualifying rounds took place before the results of the previous round were known. For these draws (or in any cases where the result of a tie in the previous round was not known at the time of the draw), the seeding was carried out under the assumption that the team with the higher coefficient of an undecided tie advanced to this round, which means if the team with the lower coefficient was to advance, it simply took the seeding of its defeated opponent. Prior to the draws, UEFA may form "groups" in accordance with the principles set by the Club Competitions Committee, but they are purely for convenience of the draw and for ensuring that teams from the same association are not drawn against each other, and do not resemble any real groupings in the sense of the competition.

A total of 154 teams were involved in the qualifying phase and play-off round (including the 15 losers of the Champions League third qualifying round which enter the play-off round). The 22 winners of the play-off round advanced to the group stage to join the 16 teams which enter in the group stage and the 10 losers of the Champions League play-off round.

Below are the participating teams (with their 2016 UEFA club coefficients),{{cite web |title=Club coefficients 2015/16 |url=http://www.uefa.com/memberassociations/uefarankings/club/season=2016/index.html |archive-url=https://archive.today/20150602191640/http://www.uefa.com/memberassociations/uefarankings/club/season=2016/index.html |url-status=dead |archive-date=June 2, 2015 |website=UEFA |publisher=Union of European Football Associations |access-date=12 June 2016}}{{cite web |title=UEFA Team Ranking 2016 |url=https://kassiesa.net/uefa/data/method4/trank2016.html |website=kassiesa.home.xs4all.nl |publisher=Bert Kassies |access-date=12 June 2016 |archive-date=7 December 2015 |archive-url=https://web.archive.org/web/20151207003253/http://kassiesa.home.xs4all.nl/bert/uefa/data/method4/trank2016.html |url-status=dead }} grouped by their starting rounds.{{cite web |title=2016/17 UEFA Champions League participants |url=http://www.uefa.com/uefaeuropaleague/season=2017/accesslist/listofparticipants/index.html |archive-url=https://web.archive.org/web/20160324012240/http://www.uefa.com/uefaeuropaleague/season=2017/accesslist/listofparticipants/index.html |url-status=dead |archive-date=March 24, 2016 |website=UEFA |publisher=Union of European Football Associations |access-date=12 June 2016}}{{cite web |url=https://www.uefa.com/uefaeuropaleague/news/022e-0e948d0b0945-24ce127f109b-1000--who-is-in-the-uefa-europa-league/ |title=Who is in the UEFA Europa League and when do they enter? |website=UEFA |publisher=Union of European Football Associations |date=20 June 2016 |access-date=20 June 2016}}

class="wikitable"
Key to colours
bgcolor=#bbf3bb |Winners of the play-off round advance to the group stage

valign=top | {| class="wikitable"
+Play-off round
Team !width=20|{{Tooltip|Coeff|UEFA Club Coefficient}}
bgcolor=#bbf3bb |{{fbaicon|UKR}} Shakhtar Donetsk{{Cref2|CL-LR}} |align=right|81.976
bgcolor=#bbf3bb |{{fbaicon|GRE}} Olympiacos{{Cref2|CL-CR}} |align=right|70.940
bgcolor=#bbf3bb |{{fbaicon|BEL}} Anderlecht{{Cref2|CL-LR}} |align=right|54.000
bgcolor=#bbf3bb |{{fbaicon|TUR}} Fenerbahçe{{Cref2|CL-LR}} |align=right|40.920
bgcolor=#bbf3bb |{{fbaicon|CZE}} Sparta Prague{{Cref2|CL-LR}} |align=right|40.585
bgcolor=#bbf3bb |{{fbaicon|GRE}} PAOK{{Cref2|CL-LR}} |align=right|37.440
{{fbaicon|BLR}} BATE Borisov{{Cref2|CL-CR}} |align=right|34.000
bgcolor=#bbf3bb |{{fbaicon|AZE}} Qarabağ{{Cref2|CL-CR}} |align=right|13.475
{{fbaicon|NOR}} Rosenborg{{Cref2|CL-CR}} |align=right|12.850
bgcolor=#bbf3bb |{{fbaicon|KAZ}} Astana{{Cref2|CL-CR}} |align=right|12.575
bgcolor=#bbf3bb |{{fbaicon|ROU}} Astra Giurgiu{{Cref2|CL-CR}} |align=right|11.076
{{fbaicon|SRB}} Red Star Belgrade{{Cref2|CL-CR}} |align=right|7.175
{{fbaicon|GEO}} Dinamo Tbilisi{{Cref2|CL-CR}} |align=right|5.875
{{fbaicon|SVK}} Trenčín{{Cref2|CL-CR}} |align=right|5.400
{{fbaicon|ALB}} Partizani{{Cref2|CL-CR}} |align=right|1.575

|

class="wikitable"
+Third qualifying round
Team !width=20|{{Tooltip|Coeff|UEFA Club Coefficient}}
bgcolor=#bbf3bb |{{fbaicon|NED}} AZ |align=right|43.612
{{fbaicon|FRA}} Lille |align=right|29.549
bgcolor=#bbf3bb |{{fbaicon|FRA}} Saint-Étienne |align=right|26.049
bgcolor=#bbf3bb |{{fbaicon|BEL}} Gent |align=right|25.000
bgcolor=#bbf3bb |{{fbaicon|RUS}} Krasnodar |align=right|24.216
bgcolor=#bbf3bb |{{fbaicon|AUT}} Rapid Wien |align=right|23.520
bgcolor=#bbf3bb |{{fbaicon|CZE}} Slovan Liberec |align=right|22.085
{{fbaicon|RUS}} Spartak Moscow |align=right|19.216
{{fbaicon|ENG}} West Ham United |align=right|16.256
{{fbaicon|GER}} Hertha BSC |align=right|16.035
bgcolor=#bbf3bb |{{fbaicon|GRE}} Panathinaikos |align=right|14.940
{{fbaicon|CRO}} Rijeka |align=right|14.275
bgcolor=#bbf3bb |{{fbaicon|ITA}} Sassuolo |align=right|14.087
{{fbaicon|POR}} Rio Ave |align=right|13.616
{{fbaicon|UKR}} Vorskla Poltava |align=right|11.976
{{fbaicon|POR}} Arouca |align=right|10.616
{{fbaicon|CYP}} Apollon Limassol |align=right|10.435
{{fbaicon|CZE}} Mladá Boleslav |align=right|10.085
{{fbaicon|UKR}} Oleksandriya |align=right|8.976
{{fbaicon|SUI}} Luzern |align=right|8.775
{{fbaicon|GRE}} AEK Athens |align=right|7.940
{{fbaicon|TUR}} İstanbul Başakşehir |align=right|7.920
{{fbaicon|NED}} Heracles Almelo |align=right|7.112
{{fbaicon|ROU}} Pandurii Târgu Jiu |align=right|7.076
{{fbaicon|ROU}} Viitorul Constanța |align=right|5.076

|

class="wikitable"
+Second qualifying round
Team !width=20|{{Tooltip|Coeff|UEFA Club Coefficient}}
bgcolor=#bbf3bb |{{fbaicon|BEL}} Genk |align=right|36.000
{{fbaicon|SVN}} Maribor |align=right|21.625
bgcolor=#bbf3bb |{{fbaicon|AUT}} Austria Wien |align=right|19.020
{{fbaicon|SRB}} Partizan |align=right|16.925
{{fbaicon|ISR}} Maccabi Haifa |align=right|11.725
{{fbaicon|CRO}} Hajduk Split |align=right|10.775
{{fbaicon|SUI}} Grasshopper |align=right|9.755
{{fbaicon|NOR}} Strømsgodset |align=right|7.850
bgcolor=#bbf3bb |{{fbaicon|TUR}} Osmanlıspor |align=right|6.920
{{fbaicon|CZE}} Slavia Prague |align=right|6.585
{{fbaicon|SWE}} BK Häcken |align=right|5.975
{{fbaicon|GRE}} PAS Giannina |align=right|5.940
{{fbaicon|ROU}} CSM Politehnica Iași |align=right|5.076
{{fbaicon|POL}} Piast Gliwice |align=right|5.000
{{fbaicon|BUL}} Levski Sofia |align=right|4.375
{{fbaicon|BLR}} Torpedo-BelAZ Zhodino |align=right|4.250
{{fbaicon|SCO}} Hibernian |align=right|3.960
{{fbaicon|DEN}} SønderjyskE |align=right|3.720

|

class="wikitable"
+First qualifying round
Team !width=20|{{Tooltip|Coeff|UEFA Club Coefficient}}
bgcolor=#bbf3bb |{{fbaicon|ISR}} Maccabi Tel Aviv |align=right|20.225
{{fbaicon|DEN}} Midtjylland |align=right|14.720
{{fbaicon|FIN}} HJK |align=right|10.980
{{fbaicon|BLR}} Dinamo Minsk |align=right|10.000
{{fbaicon|CYP}} Omonia |align=right|9.935
{{fbaicon|AZE}} Neftçi |align=right|9.725
{{fbaicon|CYP}} AEK Larnaca |align=right|9.435
{{fbaicon|SWE}} AIK |align=right|8.975
{{fbaicon|SVK}} Slovan Bratislava |align=right|8.900
{{fbaicon|HUN}} Videoton |align=right|8.725
{{fbaicon|KAZ}} Aktobe |align=right|8.075
{{fbaicon|SRB}} Vojvodina |align=right|7.925
{{fbaicon|BLR}} Shakhtyor Soligorsk |align=right|7.500
{{fbaicon|SVK}} Spartak Trnava |align=right|7.400
{{fbaicon|DEN}} Brøndby |align=right|7.220
{{fbaicon|SWE}} IFK Göteborg |align=right|6.475
{{fbaicon|HUN}} Debrecen |align=right|6.475
{{fbaicon|SCO}} Heart of Midlothian |align=right|6.460
{{fbaicon|LVA}} Ventspils |align=right|6.075
{{fbaicon|AUT}} Admira Wacker Mödling |align=right|6.020
{{fbaicon|CRO}} Lokomotiva Zagreb |align=right|5.775
{{fbaicon|ISL}} KR |align=right|5.750
{{fbaicon|GEO}} Dila Gori |align=right|5.625
{{fbaicon|SCO}} Aberdeen |align=right|5.460
{{fbaicon|NOR}} Odd |align=right|5.350
bgcolor=#bbf3bb |{{fbaicon|AZE}} Gabala |align=right|5.225
{{fbaicon|MKD}} Rabotnicki |align=right|5.200
{{fbaicon|LIE}} Vaduz |align=right|4.850
{{fbaicon|KAZ}} Kairat |align=right|4.825
{{fbaicon|LUX}} Differdange 03 |align=right|4.800
{{fbaicon|IRL}} Shamrock Rovers |align=right|4.590
{{fbaicon|IRL}} St Patrick's Athletic |align=right|4.590
{{fbaicon|POL}} Zagłębie Lubin |align=right|4.500
{{fbaicon|POL}} Cracovia |align=right|4.500
{{fbaicon|NIR}} Linfield |align=right|4.400
{{fbaicon|MDA}} Dacia Chișinău |align=right|4.325
{{fbaicon|ISR}} Beitar Jerusalem |align=right|4.225
{{fbaicon|NOR}} Stabæk |align=right|4.100
{{fbaicon|ALB}} Kukësi |align=right|4.075
{{fbaicon|SRB}} Čukarički |align=right|3.925
{{fbaicon|EST}} Levadia Tallinn |align=right|3.850
{{fbaicon|EST}} Nõmme Kalju |align=right|3.850
{{fbaicon|ARM}} Pyunik |align=right|3.825
{{fbaicon|MDA}} Zimbru Chișinău |align=right|3.825
{{fbaicon|ISL}} Breiðablik |align=right|3.750
{{fbaicon|BIH}} Široki Brijeg |align=right|3.675
{{fbaicon|BUL}} Beroe Stara Zagora |align=right|3.625
{{fbaicon|SVN}} Domžale |align=right|3.625
{{fbaicon|KAZ}} Ordabasy |align=right|3.575
{{fbaicon|LUX}} Fola Esch |align=right|3.550
{{fbaicon|NIR}} Cliftonville |align=right|3.400
{{fbaicon|MNE}} Rudar Pljevlja |align=right|3.225
{{fbaicon|FRO}} HB |align=right|3.225
{{fbaicon|SVN}} Gorica |align=right|3.125
{{fbaicon|GEO}} Chikhura Sachkhere |align=right|3.125
{{fbaicon|ARM}} Shirak |align=right|3.075
{{fbaicon|MNE}} Budućnost Podgorica |align=right|2.975
{{fbaicon|AZE}} Kapaz |align=right|2.975
{{fbaicon|MLT}} Birkirkara |align=right|2.966
{{fbaicon|MKD}} Shkëndija |align=right|2.950
{{fbaicon|FRO}} Víkingur Gøta |align=right|2.725
{{fbaicon|BUL}} Slavia Sofia |align=right|2.625
{{fbaicon|HUN}} MTK Budapest |align=right|2.475
{{fbaicon|MLT}} Hibernians |align=right|2.466
{{fbaicon|SVK}} Spartak Myjava |align=right|2.400
{{fbaicon|LTU}} Sūduva |align=right|2.175
{{fbaicon|LUX}} Jeunesse Esch |align=right|2.050
{{fbaicon|FIN}} RoPS |align=right|1.980
{{fbaicon|LVA}} Jelgava |align=right|1.825
{{fbaicon|ALB}} Teuta |align=right|1.825
{{fbaicon|MDA}} Zaria Bălți |align=right|1.825
{{fbaicon|ISL}} Valur |align=right|1.750
{{fbaicon|FIN}} Mariehamn |align=right|1.730
{{fbaicon|AND}} Lusitanos |align=right|1.699
{{fbaicon|LTU}} Atlantas |align=right|1.675
{{fbaicon|GEO}} Samtredia |align=right|1.625
{{fbaicon|LVA}} Spartaks Jūrmala |align=right|1.575
{{fbaicon|ALB}} Partizani{{Cref2|*}} |align=right|1.575
{{fbaicon|ARM}} Banants |align=right|1.575
{{fbaicon|FRO}} NSÍ |align=right|1.475
{{fbaicon|LTU}} Trakai |align=right|1.425
{{fbaicon|BIH}} Radnik Bijeljina |align=right|1.425
{{fbaicon|BIH}} Sloboda Tuzla |align=right|1.425
{{fbaicon|NIR}} Glenavon |align=right|1.400
{{fbaicon|IRL}} Cork City |align=right|1.340
{{fbaicon|SMR}} La Fiorita |align=right|1.316
{{fbaicon|WAL}} Bala Town |align=right|1.200
{{fbaicon|MKD}} Sileks |align=right|1.200
{{fbaicon|AND}} UE Santa Coloma |align=right|1.199
{{fbaicon|MNE}} Bokelj |align=right|0.975
{{fbaicon|MLT}} Balzan |align=right|0.966
{{fbaicon|EST}} Infonet Tallinn |align=right|0.850
{{fbaicon|SMR}} Folgore |align=right|0.816
{{fbaicon|GIB}} Europa |align=right|0.700
{{fbaicon|WAL}} Llandudno |align=right|0.700
{{fbaicon|WAL}} Connah's Quay Nomads |align=right|0.700

|}

;Notes

{{Cnote2 Begin|liststyle=disc}}

{{Cnote2|CL-CR|n=0|^CL-CR Losers of the Champions League third qualifying round (Champions Route).}}

{{Cnote2|CL-LR|n=0|^CL-LR Losers of the Champions League third qualifying round (League Route).}}

{{Cnote2|*|n=0|^* Partizani were transferred to the 2016–17 UEFA Champions League second qualifying round to replace Skënderbeu who were excluded by UEFA for match-fixing.{{cite web |url=https://www.uefa.com/uefachampionsleague/news/022f-0e9491c5366c-7f36115c125a-1000--partizani-replace-sk%D0%B5nderbeu-in-champions-league/ |title=Partizani replace Skёnderbeu in Champions League |website=UEFA |publisher=Union of European Football Associations |date=6 July 2016 |access-date=6 July 2016}}}}

{{Cnote2 End}}

A total of 96 teams played in the first qualifying round. The draw was held on 20 June 2016.{{cite web |title=Europa League first and second qualifying round draws |url=https://www.uefa.com/uefaeuropaleague/news/022e-0e948d0ae6e4-d113e1170df1-1000--europa-league-first-and-second-qualifying-round-draws/ |website=UEFA |publisher=Union of European Football Associations |date=20 June 2016 |access-date=20 June 2016}} Teams were pre-assigned numbers by UEFA so that the draw could be held in one run for all groups with ten teams and another run for the groups with eight teams.

class="wikitable" style="font-size:85%"
colspan=2|Group 1 !colspan=2|Group 2 !colspan=2|Group 3
Seeded !Unseeded !Seeded !Unseeded !Seeded !Unseeded
valign=top| {{fbaicon|DEN}} Midtjylland {{small|(5)}} {{fbaicon|SCO}} Heart of Midlothian {{small|(2)}} {{fbaicon|LVA}} Ventspils {{small|(4)}} {{fbaicon|NIR}} Linfield {{small|(3)}} {{fbaicon|NOR}} Stabæk {{small|(1)}} |valign=top| {{fbaicon|FRO}} Víkingur Gøta {{small|(6)}} {{fbaicon|LTU}} Sūduva {{small|(7)}} {{fbaicon|IRL}} Cork City {{small|(8)}} {{fbaicon|EST}} Infonet Tallinn {{small|(9)}} {{fbaicon|WAL}} Connah's Quay Nomads {{small|(10)}} |valign=top| {{fbaicon|FIN}} HJK {{small|(2)}} {{fbaicon|SWE}} IFK Göteborg {{small|(1)}} {{fbaicon|ISL}} KR {{small|(3)}} {{fbaicon|IRL}} St Patrick's Athletic {{small|(4)}} {{fbaicon|EST}} Levadia Tallinn {{small|(5)}} |valign=top| {{fbaicon|FRO}} HB {{small|(7)}} {{fbaicon|LUX}} Jeunesse Esch {{small|(6)}} {{fbaicon|LTU}} Atlantas {{small|(9)}} {{fbaicon|NIR}} Glenavon {{small|(8)}} {{fbaicon|WAL}} Llandudno {{small|(10)}} |valign=top| {{fbaicon|BLR}} Dinamo Minsk {{small|(3)}} {{fbaicon|DEN}} Brøndby {{small|(2)}} {{fbaicon|SCO}} Aberdeen {{small|(1)}} {{fbaicon|IRL}} Shamrock Rovers {{small|(5)}} {{fbaicon|EST}} Nõmme Kalju {{small|(4)}} |valign=top| {{fbaicon|LUX}} Fola Esch {{small|(10)}} {{fbaicon|FIN}} RoPS {{small|(7)}} {{fbaicon|ISL}} Valur {{small|(9)}} {{fbaicon|LVA}} Spartaks Jūrmala {{small|(8)}} {{fbaicon|LTU}} Trakai {{small|(6)}}
colspan=2|Group 4 !colspan=2|Group 5 !colspan=2|Group 6
Seeded !Unseeded !Seeded !Unseeded !Seeded !Unseeded
valign=top| {{fbaicon|SWE}} AIK {{small|(1)}} {{fbaicon|BLR}} Shakhtyor Soligorsk {{small|(2)}} {{fbaicon|NOR}} Odd {{small|(3)}} {{fbaicon|LUX}} Differdange 03 {{small|(4)}} {{fbaicon|ISL}} Breiðablik {{small|(5)}} |valign=top| {{fbaicon|NIR}} Cliftonville {{small|(6)}} {{fbaicon|LVA}} Jelgava {{small|(7)}} {{fbaicon|FIN}} Mariehamn {{small|(8)}} {{fbaicon|FRO}} NSÍ {{small|(9)}} {{fbaicon|WAL}} Bala Town {{small|(10)}} |valign=top| {{fbaicon|CYP}} AEK Larnaca {{small|(1)}} {{fbaicon|SRB}} Vojvodina {{small|(2)}} {{fbaicon|GEO}} Dila Gori {{small|(4)}} {{fbaicon|BIH}} Široki Brijeg {{small|(3)}} {{fbaicon|SVN}} Domžale {{small|(5)}} |valign=top| {{fbaicon|ARM}} Shirak {{small|(6)}} {{fbaicon|MLT}} Birkirkara {{small|(8)}} {{fbaicon|AND}} Lusitanos {{small|(7)}} {{fbaicon|MNE}} Bokelj {{small|(9)}} {{fbaicon|SMR}} Folgore {{small|(10)}} |valign=top| {{fbaicon|HUN}} Videoton {{small|(5)}} {{fbaicon|CRO}} Lokomotiva Zagreb {{small|(2)}} {{fbaicon|MKD}} Rabotnicki {{small|(3)}} {{fbaicon|SRB}} Čukarički {{small|(4)}} {{fbaicon|ARM}} Pyunik {{small|(1)}} |valign=top| {{fbaicon|KAZ}} Ordabasy {{small|(6)}} {{fbaicon|MNE}} Budućnost Podgorica {{small|(8)}} {{fbaicon|MDA}} Zaria Bălți {{small|(7)}} {{fbaicon|AND}} UE Santa Coloma {{small|(9)}} {{fbaicon|GIB}} Europa {{small|(10)}}
colspan=2|Group 7 !colspan=2|Group 8 !colspan=2|Group 9
Seeded !Unseeded !Seeded !Unseeded !Seeded !Unseeded
valign=top| {{fbaicon|AZE}} Neftçi {{small|(4)}} {{fbaicon|AUT}} Admira Wacker Mödling {{small|(3)}} {{fbaicon|ISR}} Beitar Jerusalem {{small|(2)}} {{fbaicon|ALB}} Kukësi {{small|(1)}} {{fbaicon|MDA}} Zimbru Chișinău {{small|(5)}} |valign=top| {{fbaicon|MNE}} Rudar Pljevlja {{small|(10)}} {{fbaicon|GEO}} Chikhura Sachkhere {{small|(7)}} {{fbaicon|SVK}} Spartak Myjava {{small|(8)}} {{fbaicon|BIH}} Sloboda Tuzla {{small|(9)}} {{fbaicon|MLT}} Balzan {{small|(6)}} |valign=top| {{fbaicon|ISR}} Maccabi Tel Aviv {{small|(4)}} {{fbaicon|HUN}} Debrecen {{small|(2)}} {{fbaicon|AZE}} Gabala {{small|(3)}} {{fbaicon|LIE}} Vaduz {{small|(1)}} {{fbaicon|BUL}} Beroe Stara Zagora {{small|(5)}} |valign=top| {{fbaicon|SVN}} Gorica {{small|(6)}} {{fbaicon|GEO}} Samtredia {{small|(8)}} {{fbaicon|BIH}} Radnik Bijeljina {{small|(7)}} {{fbaicon|SMR}} La Fiorita {{small|(9)}} {{fbaicon|MKD}} Sileks {{small|(10)}} |valign=top| {{fbaicon|CYP}} Omonia {{small|(4)}} {{fbaicon|SVK}} Spartak Trnava {{small|(2)}} {{fbaicon|KAZ}} Kairat {{small|(3)}} {{fbaicon|POL}} Cracovia {{small|(1)}} |valign=top| {{fbaicon|MKD}} Shkëndija {{small|(5)}} {{fbaicon|MLT}} Hibernians {{small|(7)}} {{fbaicon|ALB}} Teuta {{small|(6)}} {{fbaicon|ARM}} Banants {{small|(8)}}
colspan=2|Group 10 !rowspan=3 colspan=4|
Seeded !Unseeded
valign=top| {{fbaicon|SVK}} Slovan Bratislava {{small|(4)}} {{fbaicon|KAZ}} Aktobe {{small|(2)}} {{fbaicon|POL}} Zagłębie Lubin {{small|(3)}} {{fbaicon|MDA}} Dacia Chișinău {{small|(1)}} |valign=top| {{fbaicon|AZE}} Kapaz {{small|(5)}} {{fbaicon|BUL}} Slavia Sofia {{small|(6)}} {{fbaicon|HUN}} MTK Budapest {{small|(7)}} {{fbaicon|ALB}} Partizani {{small|(8)}}

The first legs were played on 28 and 30 June, and the second legs were played on 5, 6 and 7 July 2016.

{{#invoke:Sports series|main|generate_links=y

|Midtjylland|DEN|2–0|Sūduva|LTU|1–0|1–0

|Heart of Midlothian|SCO|6–3|Infonet Tallinn|EST|2–1|4–2

|Connah's Quay Nomads|WAL|1–0|Stabæk|NOR|0–0|1–0

|Ventspils|LVA|4–0|Víkingur Gøta|FRO|2–0|2–0

|Linfield|NIR|1–2|Cork City|IRL|0–1|1–1

|Levadia Tallinn|EST|3–1|HB|FRO|1–1|2–0

|Atlantas|LTU|1–3|HJK|FIN|0–2|1–1

|IFK Göteborg|SWE|7–1|Llandudno|WAL|5–0|2–1

|St Patrick's Athletic|IRL|2–2 (a)|Jeunesse Esch|LUX|1–0|1–2

|KR|ISL|8–1|Glenavon|NIR|2–1|6–0

|Shamrock Rovers|IRL|1–3|RoPS|FIN|0–2|1–1

|Valur|ISL|1–10|Brøndby|DEN|1–4|0–6

|Aberdeen|SCO|3–2|Fola Esch|LUX|3–1|0–1

|Trakai|LTU|3–5|Nõmme Kalju|EST|2–1|1–4

|Dinamo Minsk|BLR|4–1|Spartaks Jūrmala|LVA|2–1|2–0

|Breiðablik|ISL|4–5|Jelgava|LVA|2–3|2–2

|NSÍ|FRO|0–7|Shakhtyor Soligorsk|BLR|0–2|0–5

|AIK|SWE|4–0|Bala Town|WAL|2–0|2–0

|Differdange 03|LUX|1–3|Cliftonville|NIR|1–1|0–2

|Odd|NOR|3–1|Mariehamn|FIN|2–0|1–1

|Domžale|SVN|5–2|Lusitanos|AND|3–1|2–1

|Bokelj|MNE|1–6|Vojvodina|SRB|1–1|0–5

|AEK Larnaca|CYP|6–1|Folgore|SMR|3–0|3–1

|Dila Gori|GEO|1–1 (1–4 p)|Shirak|ARM|1–0|0–1 (aet)

|Široki Brijeg|BIH|1–3|Birkirkara|MLT|1–1|0–2

|Videoton|HUN|3–2|Zaria Bălți|MDA|3–0|0–2

|UE Santa Coloma|AND|2–7|Lokomotiva Zagreb|CRO|1–3|1–4

|Europa|GIB|3–2|Pyunik|ARM|2–0|1–2

|Čukarički|SRB|6–3|Ordabasy|KAZ|3–0|3–3

|Rabotnicki|MKD|1–2|Budućnost Podgorica|MNE|1–1|0–1

|Zimbru Chișinău|MDA|3–3 (a)|Chikhura Sachkhere|GEO|0–1|3–2

|Sloboda Tuzla|BIH|0–1|Beitar Jerusalem|ISR|0–0|0–1

|Kukësi|ALB|2–1|Rudar Pljevlja|MNE|1–1|1–0

|Balzan|MLT|2–3|Neftçi|AZE|0–2|2–1

|Admira Wacker Mödling|AUT|4–3|Spartak Myjava|SVK|1–1|3–2

|Beroe Stara Zagora|BUL|2–0|Radnik Bijeljina|BIH|0–0|2–0

|La Fiorita|SMR|0–7|Debrecen|HUN|0–5|0–2

|Vaduz|LIE|5–2|Sileks|MKD|3–1|2–1

|Maccabi Tel Aviv|ISR|4–0|Gorica|SVN|3–0|1–0

|Gabala|AZE|6–3|Samtredia|GEO|5–1|1–2

|Teuta|ALB|0–6|Kairat|KAZ|0–1|0–5

|Spartak Trnava|SVK|6–0|Hibernians|MLT|3–0|3–0

|Banants|ARM|1–5|Omonia|CYP|0–1|1–4 (aet)

|Shkëndija|MKD|4–1|Cracovia|POL|2–0|2–1

|Slavia Sofia|BUL|1–3|Zagłębie Lubin|POL|1–0|0–3

|Aktobe|KAZ|1–3|MTK Budapest|HUN|1–1|0–2

|Partizani|ALB|w/o|Slovan Bratislava|SVK|0–0|Canc.

|Kapaz|AZE|1–0|Dacia Chișinău|MDA|0–0|1–0

|note_agg_2=Order of legs reversed after original draw.

|note_agg_3=agg_2

|note_agg_14=agg_2

|note_agg_28=agg_2

|note_agg_34=agg_2

|note_agg_47=Partizani replaced Skënderbeu in the 2016–17 UEFA Champions League second qualifying round and Slovan Bratislava proceeded directly to the UEFA Europa League second qualifying round, after Skënderbeu was excluded by UEFA for match-fixing.{{cite web |url=https://www.uefa.com/uefachampionsleague/news/022f-0e9491c5366c-7f36115c125a-1000--partizani-replace-sk%D0%B5nderbeu-in-champions-league/ |title=Partizani replace Skёnderbeu in Champions League |website=UEFA |publisher=Union of European Football Associations |date=6 July 2016 |access-date=6 July 2016}}

|note_leg2_47=agg_47

}}

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 19:00

|team1 = Midtjylland {{fbaicon|DEN}}

|score = 1–0

|team2 = {{fbaicon|LTU}} Sūduva

|goals1 =

• Onuachu {{goal|56}}

|goals2 =

|stadium = MCH Arena, Herning

|attendance = 4,347{{cite web |title=Summary UEFA Europa League - Round 1 |url=https://int.soccerway.com/international/europe/uefa-cup/20162017/1st-qualifying-round/r35523/ |publisher=Soccerway |access-date=2 July 2016}}

|referee = Srđan Jovanović (Serbia)

|report = https://www.uefa.com/uefaeuropaleague/match/2019966/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 19:00

|team1 = Sūduva {{fbaicon|LTU}}

|score = 0–1

|team2 = {{fbaicon|DEN}} Midtjylland

|goals1 =

|goals2 =

• Novák {{goal|16}}

|stadium = Sūduva Stadium, Marijampolė

|attendance = 1,738

|referee = Peter Kralović (Slovakia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020018/

}}

Midtjylland won 2–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 21:00

|team1 = Heart of Midlothian {{fbaicon|SCO}}

|score = 2–1

|team2 = {{fbaicon|EST}} Infonet Tallinn

|goals1 =

• Buaben {{goal|28|pen.}}
• Kalimullin {{goal|36|o.g.}}

|goals2 =

• Kharin {{goal|21}}

|stadium = Tynecastle Stadium, Edinburgh

|attendance = 14,417

|referee = Vilhjálmur Alvar Þórarinsson (Iceland)

|report = https://www.uefa.com/uefaeuropaleague/match/2019967/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|6|df=y}}

|time = 17:45

|team1 = Infonet Tallinn {{fbaicon|EST}}

|score = 2–4

|team2 = {{fbaicon|SCO}} Heart of Midlothian

|goals1 =

• Kharin {{goal|51}}
• Voskoboinikov {{goal|63}}

|goals2 =

• Paterson {{goal|2}}
• Rossi {{goal|9||52}}
• Öztürk {{goal|45+1}}

|stadium = A. Le Coq Arena, Tallinn{{refn|group=note|name=Infonet Tallinn|Infonet Tallinn played their home match at A. Le Coq Arena, Tallinn, instead of their regular stadium Lasnamäe KJH Stadium, Tallinn.{{cite web |title=UEFA switch Infonet' Europa League first leg clash to Tynecastle |url=http://fcinfonet.com/en/2016/06/20/uefa-switch-infonet-europa-league-first-leg-clash-to-tynecastle/ |website=fcinfonet.com/en |publisher=FC Infonet |date=21 June 2016 |access-date=21 June 2016}}}}

|attendance = 1,354

|referee = Petr Ardeleanu (Czech Republic)

|report = https://www.uefa.com/uefaeuropaleague/match/2020019/

}}

Heart of Midlothian won 6–3 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 20:15

|team1 = Connah's Quay Nomads {{fbaicon|WAL}}

|score = 0–0

|team2 = {{fbaicon|NOR}} Stabæk

|goals1 =

|goals2 =

|stadium = Belle Vue, Rhyl{{refn|group=note|name=Connah's Quay Nomads|Connah's Quay Nomads played their home matches at Belle Vue, Rhyl, instead of their regular stadium Deeside Stadium, Connah's Quay.{{cite web |title=Nomads to face Stabæk in historic first European tie |url=http://www.the-nomads.co.uk/news/newsarticle.php?id=663 |website=www.the-nomads.co.uk |publisher=Connah's Quay Nomads F.C. |date=21 June 2016 |access-date=21 June 2016 |archive-date=11 August 2016 |archive-url=https://web.archive.org/web/20160811200741/http://www.the-nomads.co.uk/news/newsarticle.php?id=663 |url-status=dead }}}}

|attendance = 573

|referee = Johnny Casanova (San Marino)

|report = https://www.uefa.com/uefaeuropaleague/match/2019968/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 19:00

|team1 = Stabæk {{fbaicon|NOR}}

|score = 0–1

|team2 = {{fbaicon|WAL}} Connah's Quay Nomads

|goals1 =

|goals2 =

• Morris {{goal|15}}

|stadium = Fredrikstad Stadion, Fredrikstad{{refn|group=note|name=Stabæk|Stabæk played their home match at Fredrikstad Stadion, Fredrikstad, instead of their regular stadium Nadderud Stadion, Bærum.{{cite web |title=Bekreftet: Stabæk åpner borte |trans-title=Confirmed: Stabæk opens away |language=no |url=http://www.stabak.no/news/article/2gyul9o1zsqo17b2lfal0h51z/title/bekreftet-stabaek-apner-borte |website=www.stabak.no |publisher=Stabæk Fotball |date=21 June 2016 |access-date=21 June 2016 |url-status=dead |archive-url=https://web.archive.org/web/20160626204357/http://www.stabak.no/news/article/2gyul9o1zsqo17b2lfal0h51z/title/bekreftet-stabaek-apner-borte |archive-date=26 June 2016}}}}

|attendance = 384

|referee = Laurent Kopriwa (Luxembourg)

|report = https://www.uefa.com/uefaeuropaleague/match/2020020/

}}

Connah's Quay Nomads won 1–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 17:00

|team1 = Ventspils {{fbaicon|LVA}}

|score = 2–0

|team2 = {{fbaicon|FRO}} Víkingur Gøta

|goals1 =

• Karlsons {{goal|5||37}}

|goals2 =

|stadium = Olimpiskais Stadions, Ventspils

|attendance = 1,982

|referee = Mikhail Vilkov (Russia)

|report = https://www.uefa.com/uefaeuropaleague/match/2019969/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 20:00

|team1 = Víkingur Gøta {{fbaicon|FRO}}

|score = 0–2

|team2 = {{fbaicon|LVA}} Ventspils

|goals1 =

|goals2 =

• Jemeļins {{goal|57|pen.}}
• Karlsons {{goal|90+2}}

|stadium = Svangaskarð, Toftir{{refn|group=note|name=Víkingur Gøta|Víkingur Gøta played their home match at Svangaskarð, Toftir, instead of their regular stadium Sarpugerði, Norðragøta.}}

|attendance = 369

|referee = Nikolaj Hänni (Switzerland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020021/

}}

Ventspils won 4–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 20:45

|team1 = Linfield {{fbaicon|NIR}}

|score = 0–1

|team2 = {{fbaicon|IRL}} Cork City

|goals1 =

|goals2 =

• Maguire {{goal|63|pen.}}

|stadium = Windsor Park, Belfast

|attendance = 2,093

|referee = Bart Vertenten (Belgium)

|report = https://www.uefa.com/uefaeuropaleague/match/2019970/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 20:45

|team1 = Cork City {{fbaicon|IRL}}

|score = 1–1

|team2 = {{fbaicon|NIR}} Linfield

|goals1 =

• Maguire {{goal|49|pen.}}

|goals2 =

• Stafford {{goal|52}}

|stadium = Turners Cross, Cork

|attendance = 3,521

|referee = Bartosz Frankowski (Poland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020022/

}}

Cork City won 2–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 18:00

|team1 = Levadia Tallinn {{fbaicon|EST}}

|score = 1–1

|team2 = {{fbaicon|FRO}} HB

|goals1 =

• Marin {{goal|65}}

|goals2 =

• Manga {{goal|21|o.g.}}

|stadium = Kadriorg Stadium, Tallinn

|attendance = 730

|referee = Filip Glova (Slovakia)

|report = https://www.uefa.com/uefaeuropaleague/match/2019971/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 17:00

|team1 = HB {{fbaicon|FRO}}

|score = 0–2

|team2 = {{fbaicon|EST}} Levadia Tallinn

|goals1 =

|goals2 =

• Kobzar {{goal|71}}
• Miranchuk {{goal|90+2}}

|stadium = Gundadalur, Tórshavn

|attendance = 580

|referee = Radek Příhoda (Czech Republic)

|report = https://www.uefa.com/uefaeuropaleague/match/2020023/

}}

Levadia Tallinn won 3–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 18:00

|team1 = Atlantas {{fbaicon|LTU}}

|score = 0–2

|team2 = {{fbaicon|FIN}} HJK

|goals1 =

|goals2 =

• Morelos {{goal|53||85}}

|stadium = Central Stadium, Klaipėda

|attendance = 2,500

|referee = Alexandros Aretopoulos (Greece)

|report = https://www.uefa.com/uefaeuropaleague/match/2019972/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:00

|team1 = HJK {{fbaicon|FIN}}

|score = 1–1

|team2 = {{fbaicon|LTU}} Atlantas

|goals1 =

• Taiwo {{goal|30|pen.}}

|goals2 =

• Papšys {{goal|76}}

|stadium = Sonera Stadium, Helsinki

|attendance = 3,501

|referee = Bryn Markham-Jones (Wales)

|report = https://www.uefa.com/uefaeuropaleague/match/2020024/

}}

HJK won 3–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 18:30

|team1 = IFK Göteborg {{fbaicon|SWE}}

|score = 5–0

|team2 = {{fbaicon|WAL}} Llandudno

|goals1 =

• Engvall {{goal|11}}
• Rieks {{goal|12}}
• Salomonsson {{goal|36}}
• Hysén {{goal|79||81}}

|goals2 =

|stadium = Gamla Ullevi, Gothenburg

|attendance = 6,074

|referee = Martin Lundby (Norway)

|report = https://www.uefa.com/uefaeuropaleague/match/2019973/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 20:00

|team1 = Llandudno {{fbaicon|WAL}}

|score = 1–2

|team2 = {{fbaicon|SWE}} IFK Göteborg

|goals1 =

• Hughes {{goal|72}}

|goals2 =

• Smedberg-Dalence {{goal|36}}
• Sköld {{goal|54}}

|stadium = Nantporth, Bangor{{refn|group=note|name=Llandudno|Llandudno played their home match at Nantporth, Bangor, instead of their regular stadium Maesdu Park, Llandudno.{{cite web |title=Tough draws for Welsh Premier sides in Europa League |url=http://www.dailypost.co.uk/sport/football/football-news/tough-draws-welsh-premier-sides-11498235 |website=dailypost.co.uk |publisher=Daily Post |date=20 June 2016 |access-date=20 June 2016}}}}

|attendance = 841

|referee = Tiago Martins (Portugal)

|report = https://www.uefa.com/uefaeuropaleague/match/2020025/

}}

IFK Göteborg won 7–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|28|df=y}}

|time = 20:45

|team1 = St Patrick's Athletic {{fbaicon|IRL}}

|score = 1–0

|team2 = {{fbaicon|LUX}} Jeunesse Esch

|goals1 =

• Fagan {{goal|10}}

|goals2 =

|stadium = Richmond Park, Dublin

|attendance = 1,200

|referee = Pavel Orel (Czech Republic)

|report = https://www.uefa.com/uefaeuropaleague/match/2019974/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|5|df=y}}

|time = 18:45

|team1 = Jeunesse Esch {{fbaicon|LUX}}

|score = 2–1

|team2 = {{fbaicon|IRL}} St Patrick's Athletic

|goals1 =

• Stumpf {{goal|22||87}}

|goals2 =

• D. Dennehy {{goal|73}}

|stadium = Stade de la Frontière, Esch-sur-Alzette

|attendance = 1,378

|referee = Irfan Peljto (Bosnia and Herzegovina)

|report = https://www.uefa.com/uefaeuropaleague/match/2020026/

}}

2–2 on aggregate; St Patrick's Athletic won on away goals.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 21:15

|team1 = KR {{fbaicon|ISL}}

|score = 2–1

|team2 = {{fbaicon|NIR}} Glenavon

|goals1 =

• Pálmason {{goal|40}}
• Friðjónsson {{goal|78|pen.}}

|goals2 =

• Kelly {{goal|14}}

|stadium = KR-völlur, Reykjavík

|attendance = 502

|referee = Nicolas Laforge (Belgium)

|report = https://www.uefa.com/uefaeuropaleague/match/2019975/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 20:45

|team1 = Glenavon {{fbaicon|NIR}}

|score = 0–6

|team2 = {{fbaicon|ISL}} KR

|goals1 =

|goals2 =

• Chopart {{goal|6||29}}
• Friðjónsson {{goal|53|pen.}}
• Andersen {{goal|68}}
• Hauksson {{goal|78}}
• Fazlagic {{goal|80}}

|stadium = Mourneview Park, Lurgan

|attendance = 1,250

|referee = Dennis Antamo (Finland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020027/

}}

KR won 8–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 21:00

|team1 = Shamrock Rovers {{fbaicon|IRL}}

|score = 0–2

|team2 = {{fbaicon|FIN}} RoPS

|goals1 =

|goals2 =

• Lahdenmäki {{goal|27}}
• Saksela {{goal|74}}

|stadium = Tallaght Stadium, Tallaght

|attendance = 1,908

|referee = Georgios Kominis (Greece)

|report = https://www.uefa.com/uefaeuropaleague/match/2019976/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:00

|team1 = RoPS {{fbaicon|FIN}}

|score = 1–1

|team2 = {{fbaicon|IRL}} Shamrock Rovers

|goals1 =

• Muinonen {{goal|27}}

|goals2 =

• McCabe {{goal|22|pen.}}

|stadium = Keskuskenttä, Rovaniemi

|attendance = 1,525

|referee = Dejan Jakimovski (Macedonia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020028/

}}

RoPS won 3–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 23:00

|team1 = Valur {{fbaicon|ISL}}

|score = 1–4

|team2 = {{fbaicon|DEN}} Brøndby

|goals1 =

• Ingvarsson {{goal|90+2}}

|goals2 =

• Wilczek {{goal|47||54}}
• Pukki {{goal|61}}
• Jakobsen {{goal|79}}

|stadium = Hlíðarendi, Reykjavík

|attendance = 728

|referee = Ali Palabıyık (Turkey)

|report = https://www.uefa.com/uefaeuropaleague/match/2019977/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:30

|team1 = Brøndby {{fbaicon|DEN}}

|score = 6–0

|team2 = {{fbaicon|ISL}} Valur

|goals1 =

• Wilczek {{goal|5}}
• Hjulsager {{goal|15}}
• Pukki {{goal|26||57}}
• Stückler {{goal|71||90+3}}

|goals2 =

|stadium = Brøndby Stadium, Brøndbyvester

|attendance = 6,227

|referee = Tihomir Pejin (Croatia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020029/

}}

Brøndby won 10–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 20:45

|team1 = Aberdeen {{fbaicon|SCO}}

|score = 3–1

|team2 = {{fbaicon|LUX}} Fola Esch

|goals1 =

• Logan {{goal|68}}
• McGinn {{goal|90+3}}
• Rooney {{goal|90+8|pen.}}

|goals2 =

• Klein {{goal|70}}

|stadium = Pittodrie Stadium, Aberdeen

|attendance = 12,570

|referee = Mads-Kristoffer Kristoffersen (Denmark)

|report = https://www.uefa.com/uefaeuropaleague/match/2019978/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:30

|team1 = Fola Esch {{fbaicon|LUX}}

|score = 1–0

|team2 = {{fbaicon|SCO}} Aberdeen

|goals1 =

• Hadji {{goal|45}}

|goals2 =

|stadium = Stade Josy Barthel, Luxembourg City{{refn|group=note|name=Fola Esch|Fola Esch played their home match at Stade Josy Barthel, Luxembourg City, instead of their regular stadium Stade Émile Mayrisch, Esch-sur-Alzette.}}

|attendance = 1,789

|referee = Ola Hobber Nilsen (Norway)

|report = https://www.uefa.com/uefaeuropaleague/match/2020030/

}}

Aberdeen won 3–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 18:00

|team1 = Trakai {{fbaicon|LTU}}

|score = 2–1

|team2 = {{fbaicon|EST}} Nõmme Kalju

|goals1 =

• Valskis {{goal|69}}
• Arshakyan {{goal|78}}

|goals2 =

• Wakui {{goal|6|pen.}}

|stadium = LFF Stadium, Vilnius

|attendance = 500

|referee = Vladimir Vnuk (Slovakia)

|report = https://www.uefa.com/uefaeuropaleague/match/2019979/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:00

|team1 = Nõmme Kalju {{fbaicon|EST}}

|score = 4–1

|team2 = {{fbaicon|LTU}} Trakai

|goals1 =

• Rodrigues {{goal|66}}
• Sidorenkov {{goal|69}}
• Neemelo {{goal|87||90+2}}

|goals2 =

• Arshakyan {{goal|14}}

|stadium = Kadriorg Stadium, Tallinn{{refn|group=note|name=Nõmme Kalju|Nõmme Kalju played their home matches at Kadriorg Stadium, Tallinn, instead of their regular stadium Hiiu Stadium, Tallinn.}}

|attendance = 465

|referee = Erik Lambrechts (Belgium)

|report = https://www.uefa.com/uefaeuropaleague/match/2020031/

}}

Nõmme Kalju won 5–3 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 18:00

|team1 = Dinamo Minsk {{fbaicon|BLR}}

|score = 2–1

|team2 = {{fbaicon|LVA}} Spartaks Jūrmala

|goals1 =

• Bykov {{goal|18||82}}

|goals2 =

• Ulimbaševs {{goal|80}}

|stadium = Traktor Stadium, Minsk

|attendance = 1,700

|referee = Zaven Hovhannisyan (Armenia)

|report = https://www.uefa.com/uefaeuropaleague/match/2019980/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:00

|team1 = Spartaks Jūrmala {{fbaicon|LVA}}

|score = 0–2

|team2 = {{fbaicon|BLR}} Dinamo Minsk

|goals1 =

|goals2 =

• Khvashchynski {{goal|11}}
• El-Monir {{goal|90+1}}

|stadium = Slokas Stadium, Jūrmala

|attendance = 1,100

|referee = Alexandru Tean (Moldova)

|report = https://www.uefa.com/uefaeuropaleague/match/2020032/

}}

Dinamo Minsk won 4–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 21:15

|team1 = Breiðablik {{fbaicon|ISL}}

|score = 2–3

|team2 = {{fbaicon|LVA}} Jelgava

|goals1 =

• Bamberg {{goal|13}}
• Sigurjónsson {{goal|90+6}}

|goals2 =

• Kļuškins {{goal|10}}
• Redjko {{goal|33}}
• Grigaravičius {{goal|44}}

|stadium = Kópavogsvöllur, Kópavogur

|attendance = 531

|referee = Anders Poulsen (Denmark)

|report = https://www.uefa.com/uefaeuropaleague/match/2019981/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 17:30

|team1 = Jelgava {{fbaicon|LVA}}

|score = 2–2

|team2 = {{fbaicon|ISL}} Breiðablik

|goals1 =

• Turkovs {{goal|15}}
• Diallo {{goal|70}}

|goals2 =

• Hreinsson {{goal|31}}
• Bamberg {{goal|33|pen.}}

|stadium = Olympic Sports Center of Zemgale, Jelgava

|attendance = 1,560

|referee = Petur Reinert (Faroe Islands)

|report = https://www.uefa.com/uefaeuropaleague/match/2020033/

}}

Jelgava won 5–4 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 20:00

|team1 = NSÍ {{fbaicon|FRO}}

|score = 0–2

|team2 = {{fbaicon|BLR}} Shakhtyor Soligorsk

|goals1 =

|goals2 =

• Starhorodskyi {{goal|45+1|pen.|84|pen.}}

|stadium = Svangaskarð, Toftir{{refn|group=note|name=NSÍ Runavík|NSÍ Runavík played their home match at Svangaskarð, Toftir, instead of their regular stadium Runavík Stadium, Runavík.}}

|attendance = 350

|referee = Tim Marshall (Northern Ireland)

|report = https://www.uefa.com/uefaeuropaleague/match/2019982/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 20:00

|team1 = Shakhtyor Soligorsk {{fbaicon|BLR}}

|score = 5–0

|team2 = {{fbaicon|FRO}} NSÍ

|goals1 =

• Burko {{goal|20}}
• Rudyka {{goal|42}}
• Shibun {{goal|81|pen.}}
• Yelezarenko {{goal|86}}
• Yanushkevich {{goal|90}}

|goals2 =

|stadium = Stroitel Stadium, Salihorsk

|attendance = 1,100

|referee = Giorgi Vadachkoria (Georgia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020034/

}}

Shakhtyor Soligorsk won 7–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 18:30

|team1 = AIK {{fbaicon|SWE}}

|score = 2–0

|team2 = {{fbaicon|WAL}} Bala Town

|goals1 =

• Affane {{goal|27}}
• Johansson {{goal|52}}

|goals2 =

|stadium = Tele2 Arena, Stockholm{{refn|group=note|name=AIK|AIK played their first and third qualifying rounds home matches at Tele2 Arena, Stockholm, instead of their regular stadium Friends Arena, Solna.}}

|attendance = 6,127

|referee = Kirill Levnikov (Russia)

|report = https://www.uefa.com/uefaeuropaleague/match/2019983/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 19:30

|team1 = Bala Town {{fbaicon|WAL}}

|score = 0–2

|team2 = {{fbaicon|SWE}} AIK

|goals1 =

|goals2 =

• Avdić {{goal|8}}
• Strandberg {{goal|24}}

|stadium = Belle Vue, Rhyl{{refn|group=note|name=Bala Town|Bala Town played their home match at Belle Vue, Rhyl, instead of their regular stadium Maes Tegid, Bala.}}

|attendance = 890

|referee = Fedayi San (Switzerland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020035/

}}

AIK won 4–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 19:00

|team1 = Differdange 03 {{fbaicon|LUX}}

|score = 1–1

|team2 = {{fbaicon|NIR}} Cliftonville

|goals1 =

• Er Rafik {{goal|38}}

|goals2 =

• Lavery {{goal|89}}

|stadium = Stade Municipal, Differdange

|attendance = 1,355

|referee = Ignasi Villamayor Rozados (Andorra)

|report = https://www.uefa.com/uefaeuropaleague/match/2019984/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 20:45

|team1 = Cliftonville {{fbaicon|NIR}}

|score = 2–0

|team2 = {{fbaicon|LUX}} Differdange 03

|goals1 =

• McDaid {{goal|2}}
• J. Donnelly {{goal|75}}

|goals2 =

|stadium = Solitude, Belfast

|attendance = 1,168

|referee = Ferenc Karakó (Hungary)

|report = https://www.uefa.com/uefaeuropaleague/match/2020036/

}}

Cliftonville won 3–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 19:00

|team1 = Odd {{fbaicon|NOR}}

|score = 2–0

|team2 = {{fbaicon|FIN}} Mariehamn

|goals1 =

• Grøgaard {{goal|63}}
• Occéan {{goal|86}}

|goals2 =

|stadium = Skagerak Arena, Skien

|attendance = 3,701

|referee = Mohammed Al-Hakim (Sweden)

|report = https://www.uefa.com/uefaeuropaleague/match/2019985/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:00

|team1 = Mariehamn {{fbaicon|FIN}}

|score = 1–1

|team2 = {{fbaicon|NOR}} Odd

|goals1 =

• Mantilla {{goal|4}}

|goals2 =

• Bentley {{goal|78}}

|stadium = Wiklöf Holding Arena, Mariehamn

|attendance = 1,402

|referee = Peter Kjærsgaard-Andersen (Denmark)

|report = https://www.uefa.com/uefaeuropaleague/match/2020037/

}}

Odd won 3–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 20:00

|team1 = Domžale {{fbaicon|SVN}}

|score = 3–1

|team2 = {{fbaicon|AND}} Lusitanos

|goals1 =

• Dobrovoljc {{goal|11}}
• Horić {{goal|26}}
• Črnic {{goal|43}}

|goals2 =

• Luizão {{goal|5}}

|stadium = Sports Park, Domžale

|attendance = 1,000

|referee = Orkhan Mammadov (Azerbaijan)

|report = https://www.uefa.com/uefaeuropaleague/match/2019986/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 20:30

|team1 = Lusitanos {{fbaicon|AND}}

|score = 1–2

|team2 = {{fbaicon|SVN}} Domžale

|goals1 =

• Luizão {{goal|18}}

|goals2 =

• Majer {{goal|5}}
• Morel {{goal|42}}

|stadium = Estadi Comunal, Andorra la Vella

|attendance = 500

|referee = Stanislav Todorov (Bulgaria)

|report = https://www.uefa.com/uefaeuropaleague/match/2020038/

}}

Domžale won 5–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 17:30

|team1 = Bokelj {{fbaicon|MNE}}

|score = 1–1

|team2 = {{fbaicon|SRB}} Vojvodina

|goals1 =

• Đenić {{goal|5}}

|goals2 =

• Meleg {{goal|6}}

|stadium = Stadion pod Malim brdom, Petrovac{{refn|group=note|name=Bokelj|Bokelj played their home match at Stadion pod Malim brdom, Petrovac, instead of their regular stadium Stadion pod Vrmcem, Kotor.}}

|attendance = 1,403

|referee = Alejandro Hernández Hernández (Spain)

|report = https://www.uefa.com/uefaeuropaleague/match/2019987/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 20:00

|team1 = Vojvodina {{fbaicon|SRB}}

|score = 5–0

|team2 = {{fbaicon|MNE}} Bokelj

|goals1 =

• Malbašić {{goal|9||42}}
• Meleg {{goal|60}}
• Trujić {{goal|63||87}}

|goals2 =

|stadium = Karađorđe Stadium, Novi Sad

|attendance = 4,388

|referee = Andrew Dallas (Scotland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020039/

}}

Vojvodina won 6–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 19:00

|team1 = AEK Larnaca {{fbaicon|CYP}}

|score = 3–0

|team2 = {{fbaicon|SMR}} Folgore

|goals1 =

• Tričkovski {{goal|22||34}}
• Alves {{goal|31}}

|goals2 =

|stadium = Antonis Papadopoulos Stadium, Larnaca{{refn|group=note|name=AEK Larnaca|AEK Larnaca played their home matches at Antonis Papadopoulos Stadium, Larnaca, instead of their regular stadium GSZ Stadium, Larnaca.}}

|attendance = 2,100

|referee = Aleksandrs Golubevs (Latvia)

|report = https://www.uefa.com/uefaeuropaleague/match/2019988/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 20:30

|team1 = Folgore {{fbaicon|SMR}}

|score = 1–3

|team2 = {{fbaicon|CYP}} AEK Larnaca

|goals1 =

• Traini {{goal|35}}

|goals2 =

• Tričkovski {{goal|51||55}}
• Alves {{goal|65|pen.}}

|stadium = San Marino Stadium, Serravalle

|attendance = 319

|referee = Jens Maae (Denmark)

|report = https://www.uefa.com/uefaeuropaleague/match/2020040/

}}

AEK Larnaca won 6–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 16:00

|team1 = Dila Gori {{fbaicon|GEO}}

|score = 1–0

|team2 = {{fbaicon|ARM}} Shirak

|goals1 =

• Modebadze {{goal|36}}

|goals2 =

|stadium = Tengiz Burjanadze Stadium, Gori

|attendance = 2,512

|referee = Anatoliy Zhabchenko (Ukraine)

|report = https://www.uefa.com/uefaeuropaleague/match/2019989/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 15:00

|team1 = Shirak {{fbaicon|ARM}}

|score = 1–0

|aet = yes

|team2 = {{fbaicon|GEO}} Dila Gori

|goals1 =

• Bichakhchyan {{goal|84}}

|goals2 =

|stadium = City Stadium, Gyumri

|attendance = 2,400

|referee = Sergejus Slyva (Lithuania)

|penalties1 =

• Hovsepyan {{pengoal}}
• Darbinyan {{pengoal}}
• Ayvazyan {{pengoal}}
• Hakobyan {{pengoal}}

|penaltyscore = 4–1

|penalties2 =

• {{penmiss}} Gongadze
• {{penmiss}} Kvirkvelia
• {{pengoal}} Razmadze

|report = https://www.uefa.com/uefaeuropaleague/match/2020041/

}}

1–1 on aggregate; Shirak won 4–1 on penalties.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 19:00

|team1 = Široki Brijeg {{fbaicon|BIH}}

|score = 1–1

|team2 = {{fbaicon|MLT}} Birkirkara

|goals1 =

• Baraban {{goal|45}}

|goals2 =

• Attard {{goal|15}}

|stadium = Stadion Pecara, Široki Brijeg

|attendance = 3,000

|referee = Sandro Schärer (Switzerland)

|report = https://www.uefa.com/uefaeuropaleague/match/2019990/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|5|df=y}}

|time = 17:45

|team1 = Birkirkara {{fbaicon|MLT}}

|score = 2–0

|team2 = {{fbaicon|BIH}} Široki Brijeg

|goals1 =

• Dimitrov {{goal|29}}
• Marković {{goal|76|o.g.}}

|goals2 =

|stadium = Hibernians Stadium, Paola{{refn|group=note|name=Birkirkara|Birkirkara played their home matches at Hibernians Stadium, Paola, instead of their regular stadium National Stadium, Ta' Qali.}}

|attendance = 1,152

|referee = Rahim Hasanov (Azerbaijan)

|report = https://www.uefa.com/uefaeuropaleague/match/2020042/

}}

Birkirkara won 3–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 18:00

|team1 = Videoton {{fbaicon|HUN}}

|score = 3–0

|team2 = {{fbaicon|MDA}} Zaria Bălți

|goals1 =

• Géresi {{goal|18}}
• Feczesin {{goal|88||90+4}}

|goals2 =

|stadium = Pancho Arena, Felcsút{{refn|group=note|name=Videoton|Videoton played their home matches at Pancho Arena, Felcsút, instead of their regular stadium Sóstói Stadion, Székesfehérvár, due to reconstruction.{{cite web |title=Videoton: a Sóstói Stadion elemeit újrahasznosítják |trans-title=Videoton: Sóstói stadium elements will be recycled |language=hu |url=http://www.nemzetisport.hu/labdarugo_nb_i/videoton-a-sostoi-stadion-elemeit-ujrahasznositjak-2459099 |website=www.nemzetisport.hu |publisher=Nemzeti Sport |date=6 January 2016 |access-date=23 June 2016}}}}

|attendance = 2,321

|referee = Enea Jorgji (Albania)

|report = https://www.uefa.com/uefaeuropaleague/match/2019991/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 19:00

|team1 = Zaria Bălți {{fbaicon|MDA}}

|score = 2–0

|team2 = {{fbaicon|HUN}} Videoton

|goals1 =

• Mihaliov {{goal|9}}
• Ovseanicov {{goal|29}}

|goals2 =

|stadium = Zimbru Stadium, Chișinău{{refn|group=note|name=Zaria Bălți|Zaria Bălți played their home match at Zimbru Stadium, Chișinău, instead of their regular stadium Stadionul Orășenesc, Bălți.}}

|attendance = 2,097

|referee = Fyodor Zammit (Malta)

|report = https://www.uefa.com/uefaeuropaleague/match/2020043/

}}

Videoton won 3–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 17:00

|team1 = UE Santa Coloma {{fbaicon|AND}}

|score = 1–3

|team2 = {{fbaicon|CRO}} Lokomotiva Zagreb

|goals1 =

• Reis {{goal|90+3}}

|goals2 =

• Marić {{goal|20||73}}
• Prenga {{goal|65}}

|stadium = Estadi Comunal, Andorra la Vella

|attendance = 250

|referee = Donatas Rumšas (Lithuania)

|report = https://www.uefa.com/uefaeuropaleague/match/2019992/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:00

|team1 = Lokomotiva Zagreb {{fbaicon|CRO}}

|score = 4–1

|team2 = {{fbaicon|AND}} UE Santa Coloma

|goals1 =

• Ćorić {{goal|8}}
• Prenga {{goal|18|pen.}}
• Marić {{goal|48}}
• Perić {{goal|57}}

|goals2 =

• Salomó {{goal|89}}

|stadium = Stadion Kranjčevićeva, Zagreb

|attendance = 294

|referee = Veaceslav Banari (Moldova)

|report = https://www.uefa.com/uefaeuropaleague/match/2020044/

}}

Lokomotiva Zagreb won 7–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 18:30

|team1 = Europa {{fbaicon|GIB}}

|score = 2–0

|team2 = {{fbaicon|ARM}} Pyunik

|goals1 =

• Carrión {{goal|32}}
• López {{goal|39}}

|goals2 =

|stadium = Victoria Stadium, Gibraltar

|attendance = 850

|referee = Markus Hameter (Austria)

|report = https://www.uefa.com/uefaeuropaleague/match/2019993/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 17:00

|team1 = Pyunik {{fbaicon|ARM}}

|score = 2–1

|team2 = {{fbaicon|GIB}} Europa

|goals1 =

• Arakelyan {{goal|25}}
• Ra. Hakobyan {{goal|56}}

|goals2 =

• Joselinho {{goal|10}}

|stadium = Vazgen Sargsyan Republican Stadium, Yerevan{{refn|group=note|name=Pyunik|Pyunik played their home match at Vazgen Sargsyan Republican Stadium, Yerevan, instead of their regular stadium Football Academy Stadium, Yerevan.}}

|attendance = 2,000

|referee = Boris Marhefka (Slovakia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020045/

}}

Europa won 3–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 20:30

|team1 = Čukarički {{fbaicon|SRB}}

|score = 3–0

|team2 = {{fbaicon|KAZ}} Ordabasy

|goals1 =

• Matić {{goal|49|pen.|68}}
• Kajević {{goal|53}}

|goals2 =

|stadium = Čukarički Stadium, Belgrade

|attendance = 2,214

|referee = Fábio Veríssimo (Portugal)

|report = https://www.uefa.com/uefaeuropaleague/match/2019994/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 14:00

|team1 = Ordabasy {{fbaicon|KAZ}}

|score = 3–3

|team2 = {{fbaicon|SRB}} Čukarički

|goals1 =

• Geynrikh {{goal|45+2}}
• Tunggyshbayev {{goal|67}}
• Yerlanov {{goal|90+3}}

|goals2 =

• Mandić {{goal|10||14}}
• Kajević {{goal|21}}

|stadium = Kazhymukan Munaitpasov Stadium, Shymkent

|attendance = 5,100

|referee = Denis Scherbakov (Belarus)

|report = https://www.uefa.com/uefaeuropaleague/match/2020046/

}}

Čukarički won 6–3 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|28|df=y}}

|time = 18:00

|team1 = Rabotnicki {{fbaicon|MKD}}

|score = 1–1

|team2 = {{fbaicon|MNE}} Budućnost Podgorica

|goals1 =

• Elmas {{goal|80}}

|goals2 =

• Janketić {{goal|36}}

|stadium = Philip II Arena, Skopje

|attendance = 1,500

|referee = Zbyněk Proske (Czech Republic)

|report = https://www.uefa.com/uefaeuropaleague/match/2019995/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 19:00

|team1 = Budućnost Podgorica {{fbaicon|MNE}}

|score = 1–0

|team2 = {{fbaicon|MKD}} Rabotnicki

|goals1 =

• Radunović {{goal|18|pen.}}

|goals2 =

|stadium = City Stadium, Podgorica

|attendance = 2,000

|referee = Jørgen Daugbjerg Burchardt (Denmark)

|report = https://www.uefa.com/uefaeuropaleague/match/2020047/

}}

Budućnost Podgorica won 2–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 19:00

|team1 = Zimbru Chișinău {{fbaicon|MDA}}

|score = 0–1

|team2 = {{fbaicon|GEO}} Chikhura Sachkhere

|goals1 =

|goals2 =

• Tatanashvili {{goal|39}}

|stadium = Zimbru Stadium, Chișinău

|attendance = 2,500

|referee = Jari Järvinen (Finland)

|report = https://www.uefa.com/uefaeuropaleague/match/2019996/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|5|df=y}}

|time = 18:00

|team1 = Chikhura Sachkhere {{fbaicon|GEO}}

|score = 2–3

|team2 = {{fbaicon|MDA}} Zimbru Chișinău

|goals1 =

• Ivanishvili {{goal|13}}
• Kakubava {{goal|55}}

|goals2 =

• Emerson {{goal|45+2||90+3}}
• Jardan {{goal|61}}

|stadium = David Abashidze Stadium, Zestaponi{{refn|group=note|name=Chikhura Sachkhere|Chikhura Sachkhere played their home match at David Abashidze Stadium, Zestaponi, instead of their regular stadium Central Stadium, Sachkhere.}}

|attendance = 1,500

|referee = Suren Baliyan (Armenia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020048/

}}

3–3 on aggregate; Zimbru Chișinău won on away goals.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 18:00

|team1 = Sloboda Tuzla {{fbaicon|BIH}}

|score = 0–0

|team2 = {{fbaicon|ISR}} Beitar Jerusalem

|goals1 =

|goals2 =

|stadium = Bilino Polje Stadium, Zenica{{refn|group=note|name=Sloboda Tuzla|Sloboda Tuzla played their home match at Bilino Polje Stadium, Zenica, instead of their regular stadium Tušanj City Stadium, Tuzla.{{cite web |title=Protivnik iz Svetog grada |trans-title=Opponent of the Holy City |language=bs |url=http://www.fksloboda.ba/index.php/vijesti-clanci/1001-protivnik-iz-svetog-grada |website=www.fksloboda.ba |publisher=FK Sloboda Tuzla |date=20 June 2016 |access-date=21 June 2016 |url-status=dead |archive-url=https://web.archive.org/web/20161010124613/http://www.fksloboda.ba/index.php/vijesti-clanci/1001-protivnik-iz-svetog-grada |archive-date=10 October 2016 }}}}

|attendance = 2,762

|referee = Glenn Nyberg (Sweden)

|report = https://www.uefa.com/uefaeuropaleague/match/2019997/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:45

|team1 = Beitar Jerusalem {{fbaicon|ISR}}

|score = 1–0

|team2 = {{fbaicon|BIH}} Sloboda Tuzla

|goals1 =

• Atzili {{goal|66|pen.}}

|goals2 =

|stadium = Teddy Stadium, Jerusalem

|attendance = 9,010

|referee = Oleksandr Derdo (Ukraine)

|report = https://www.uefa.com/uefaeuropaleague/match/2020049/

}}

Beitar Jerusalem won 1–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 19:00

|team1 = Kukësi {{fbaicon|ALB}}

|score = 1–1

|team2 = {{fbaicon|MNE}} Rudar Pljevlja

|goals1 =

• Rangel {{goal|32}}

|goals2 =

• Radanović {{goal|71|pen.}}

|stadium = Elbasan Arena, Elbasan{{refn|group=note|name=Kukësi|Kukësi played their home matches at Elbasan Arena, Elbasan, instead of their regular stadium Zeqir Ymeri Stadium, Kukës.{{cite web |title=Sjutra protiv Rada... |trans-title=Rada tomorrow against |language=cnr |url=http://www.fkrudarpljevlja.com/index.php?IDSP=6052 |website=fkrudarpljevlja.com |publisher=FK Rudar Pljevlja |date=21 June 2016 |access-date=23 June 2016 |archive-url=https://web.archive.org/web/20160828091438/http://www.fkrudarpljevlja.com/index.php?IDSP=6052 |archive-date=28 August 2016 |url-status=dead }}}}

|attendance = 104

|referee = Roi Reinschreiber (Israel)

|report = https://www.uefa.com/uefaeuropaleague/match/2019998/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 17:30

|team1 = Rudar Pljevlja {{fbaicon|MNE}}

|score = 0–1

|team2 = {{fbaicon|ALB}} Kukësi

|goals1 =

|goals2 =

• Guri {{goal|79}}

|stadium = City Stadium, Nikšić{{refn|group=note|name=Rudar Pljevlja|Rudar Pljevlja played their home match at City Stadium, Nikšić, instead of their regular stadium City Stadium, Pljevlja.{{cite web |title=Stadion bez licence |trans-title=The stadium without a license |language=cnr |url=http://fkrudarpljevlja.com/index.php?IDSP=6046 |website=fkrudarpljevlja.com |publisher=FK Rudar Pljevlja |date=10 June 2016 |access-date=23 June 2016 |archive-url=https://web.archive.org/web/20160828122617/http://fkrudarpljevlja.com/index.php?IDSP=6046 |archive-date=28 August 2016 |url-status=dead }}}}

|attendance = 486

|referee = João Capela (Portugal)

|report = https://www.uefa.com/uefaeuropaleague/match/2020050/

}}

Kukësi won 2–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 18:00

|team1 = Balzan {{fbaicon|MLT}}

|score = 0–2

|team2 = {{fbaicon|AZE}} Neftçi

|goals1 =

|goals2 =

• Hajiyev {{goal|14}}
• R. Qurbanov {{goal|84|pen.}}

|stadium = Hibernians Stadium, Paola{{refn|group=note|name=Balzan|Balzan played their home match at Hibernians Stadium, Paola, instead of their regular stadium National Stadium, Ta' Qali.}}

|attendance = 357

|referee = Jovan Kaluđerović (Montenegro)

|report = https://www.uefa.com/uefaeuropaleague/match/2019999/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:00

|team1 = Neftçi {{fbaicon|AZE}}

|score = 1–2

|team2 = {{fbaicon|MLT}} Balzan

|goals1 =

• Jairo {{goal|20}}

|goals2 =

• Micallef {{goal|51||67}}

|stadium = Bakcell Arena, Baku

|attendance = 7,650

|referee = Yaroslav Kozyk (Ukraine)

|report = https://www.uefa.com/uefaeuropaleague/match/2020051/

}}

Neftçi won 3–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 17:00

|team1 = Admira Wacker Mödling {{fbaicon|AUT}}

|score = 1–1

|team2 = {{fbaicon|SVK}} Spartak Myjava

|goals1 =

• Bajrami {{goal|34}}

|goals2 =

• Kóňa {{goal|73}}

|stadium = NV Arena, Sankt Pölten{{refn|group=note|name=Admira Wacker Mödling|Admira Wacker Mödling played their first and second qualifying round home matches at NV Arena, Sankt Pölten, instead of their regular stadium Bundesstadion Südstadt, Maria Enzersdorf.}}

|attendance = 1,200

|referee = Fran Jović (Croatia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020000/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 17:00

|team1 = Spartak Myjava {{fbaicon|SVK}}

|score = 2–3

|team2 = {{fbaicon|AUT}} Admira Wacker Mödling

|goals1 =

• Daniel {{goal|30}}
• Pekár {{goal|89}}

|goals2 =

• Wostry {{goal|2}}
• Starkl {{goal|27}}
• Zwierschitz {{goal|57}}

|stadium = Stadium Myjava, Myjava

|attendance = 2,057

|referee = Alper Ulusoy (Turkey)

|report = https://www.uefa.com/uefaeuropaleague/match/2020052/

}}

Admira Wacker Mödling won 4–3 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 19:30

|team1 = Beroe Stara Zagora {{fbaicon|BUL}}

|score = 0–0

|team2 = {{fbaicon|BIH}} Radnik Bijeljina

|goals1 =

|goals2 =

|stadium = Beroe Stadium, Stara Zagora

|attendance = 2,918

|referee = Giorgi Kruashvili (Georgia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020001/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:00

|team1 = Radnik Bijeljina {{fbaicon|BIH}}

|score = 0–2

|team2 = {{fbaicon|BUL}} Beroe Stara Zagora

|goals1 =

|goals2 =

• Pochanski {{goal|79||80}}

|stadium = City Stadium, Banja Luka{{refn|group=note|name=Radnik Bijeljina|Radnik Bijeljina played their home match at City Stadium, Banja Luka, instead of their regular stadium City Stadium, Bijeljina.}}

|attendance = 2,832

|referee = Dimitrios Massias (Cyprus)

|report = https://www.uefa.com/uefaeuropaleague/match/2020053/

}}

Beroe Stara Zagora won 2–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 20:30

|team1 = La Fiorita {{fbaicon|SMR}}

|score = 0–5

|team2 = {{fbaicon|HUN}} Debrecen

|goals1 =

|goals2 =

• Szakály {{goal|5||83}}
• Tisza {{goal|34||49}}
• Kulcsár {{goal|89}}

|stadium = San Marino Stadium, Serravalle

|attendance = 402

|referee = Juri Frischer (Estonia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020002/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:00

|team1 = Debrecen {{fbaicon|HUN}}

|score = 2–0

|team2 = {{fbaicon|SMR}} La Fiorita

|goals1 =

• Tisza {{goal|41}}
• Holman {{goal|51}}

|goals2 =

|stadium = Nagyerdei Stadion, Debrecen

|attendance = 8,632

|referee = Stavros Mantalos (Greece)

|report = https://www.uefa.com/uefaeuropaleague/match/2020054/

}}

Debrecen won 7–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 19:00

|team1 = Vaduz {{fbaicon|LIE}}

|score = 3–1

|team2 = {{fbaicon|MKD}} Sileks

|goals1 =

• Costanzo {{goal|36||45+2}}
• Grippo {{goal|90+5}}

|goals2 =

• Mickov {{goal|86}}

|stadium = Rheinpark Stadion, Vaduz

|attendance = 928

|referee = Þóroddur Hjaltalín Jr. (Iceland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020003/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 20:00

|team1 = Sileks {{fbaicon|MKD}}

|score = 1–2

|team2 = {{fbaicon|LIE}} Vaduz

|goals1 =

• Mickov {{goal|30}}

|goals2 =

• Costanzo {{goal|89|pen.}}
• Messaoud {{goal|90+3}}

|stadium = Philip II Arena, Skopje{{refn|group=note|name=Sileks|Sileks played their home match at Philip II Arena, Skopje, instead of their regular stadium City Stadium, Kratovo.}}

|attendance = 450

|referee = Paul McLaughlin (Republic of Ireland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020055/

}}

Vaduz won 5–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 19:15

|team1 = Maccabi Tel Aviv {{fbaicon|ISR}}

|score = 3–0

|team2 = {{fbaicon|SVN}} Gorica

|goals1 =

• Igiebor {{goal|13||69}}
• Sá {{goal|45}}

|goals2 =

|stadium = Netanya Stadium, Netanya{{refn|group=note|name=Maccabi Tel Aviv|Maccabi Tel Aviv played their home matches at Netanya Stadium, Netanya, instead of their regular stadium Bloomfield Stadium, Tel Aviv, due to reconstruction.{{cite web |title=Israeli soccer star Eran Zahavi completes record transfer to Chinese club |url=http://www.jpost.com/Israel-News/Sports/Israeli-soccer-star-Eran-Zahavi-completes-record-transfer-to-Chinese-club-459060 |website=www.jpost.com |publisher=The Jerusalem Post |date=29 June 2016 |access-date=8 July 2016}}}}

|attendance = 7,982

|referee = Jonathan Lardot (Belgium)

|report = https://www.uefa.com/uefaeuropaleague/match/2020004/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:30

|team1 = Gorica {{fbaicon|SVN}}

|score = 0–1

|team2 = {{fbaicon|ISR}} Maccabi Tel Aviv

|goals1 =

|goals2 =

• Benayoun {{goal|10}}

|stadium = Sports Park, Nova Gorica

|attendance = 700

|referee = Manuel Schüttengruber (Austria)

|report = https://www.uefa.com/uefaeuropaleague/match/2020056/

}}

Maccabi Tel Aviv won 4–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 19:00

|team1 = Gabala {{fbaicon|AZE}}

|score = 5–1

|team2 = {{fbaicon|GEO}} Samtredia

|goals1 =

• Stanković {{goal|16}}
• Zenjov {{goal|19}}
• Weeks {{goal|30||69||72}}

|goals2 =

• Shergelashvili {{goal|59}}

|stadium = Bakcell Arena, Baku{{refn|group=note|name=Gabala|Gabala played their home matches at Bakcell Arena, Baku, instead of their regular stadium City Stadium, Qabala.}}

|attendance = 5,850

|referee = Denis Scherbakov (Belarus)

|report = https://www.uefa.com/uefaeuropaleague/match/2020005/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 17:00

|team1 = Samtredia {{fbaicon|GEO}}

|score = 2–1

|team2 = {{fbaicon|AZE}} Gabala

|goals1 =

• Zivzivadze {{goal|14|pen.}}
• Shergelashvili {{goal|90+2}}

|goals2 =

• Weeks {{goal|42}}

|stadium = David Abashidze Stadium, Zestaponi{{refn|group=note|name=Samtredia|Samtredia played their home match at David Abashidze Stadium, Zestaponi, instead of their regular stadium Erosi Manjgaladze Stadium, Samtredia.}}

|attendance = 847

|referee = Georgios Kyzas (Greece)

|report = https://www.uefa.com/uefaeuropaleague/match/2020057/

}}

Gabala won 6–3 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 20:00

|team1 = Teuta {{fbaicon|ALB}}

|score = 0–1

|team2 = {{fbaicon|KAZ}} Kairat

|goals1 =

|goals2 =

• Arshavin {{goal|70}}

|stadium = Niko Dovana Stadium, Durrës

|attendance = 500

|referee = Vasilis Dimitriou (Cyprus)

|report = https://www.uefa.com/uefaeuropaleague/match/2020006/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 16:45

|team1 = Kairat {{fbaicon|KAZ}}

|score = 5–0

|team2 = {{fbaicon|ALB}} Teuta

|goals1 =

• Gohou {{goal|27||61}}
• Bakayev {{goal|45+2}}
• Tawamba {{goal|72}}
• Turysbek {{goal|79}}

|goals2 =

|stadium = Central Stadium, Almaty

|attendance = 20,700

|referee = Dag Vidar Hafsås (Norway)

|report = https://www.uefa.com/uefaeuropaleague/match/2020058/

}}

Kairat won 6–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 20:15

|team1 = Spartak Trnava {{fbaicon|SVK}}

|score = 3–0

|team2 = {{fbaicon|MLT}} Hibernians

|goals1 =

• Tambe {{goal|7||83}}
• Mikovič {{goal|40}}

|goals2 =

|stadium = Štadión Antona Malatinského, Trnava

|attendance = 0{{refn|group=note|name=Spartak Trnava vs Hibernians|The Spartak Trnava v Hibernians match was played behind closed doors due to punishment by UEFA.{{cite web |title=Spartak Trnava zvládol domáci zápas s Hibernians |trans-title=Spartak Trnava get through home match with Hibernians |language=sk |url=http://sport.aktuality.sk/c/223723/video-spartak-trnava-zvladol-domaci-zapas-s-hibernians/ |website=ŠPORT.sk |date=30 June 2016 |access-date=5 July 2016}}}}

|referee = Edin Jakupović (Bosnia and Herzegovina)

|report = https://www.uefa.com/uefaeuropaleague/match/2020007/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 20:00

|team1 = Hibernians {{fbaicon|MLT}}

|score = 0–3

|team2 = {{fbaicon|SVK}} Spartak Trnava

|goals1 =

|goals2 =

• Mikovič {{goal|5}}
• Oravec {{goal|58}}
• Bello {{goal|90+2}}

|stadium = Hibernians Stadium, Paola

|attendance = 322

|referee = Anastasios Papapetrou (Greece)

|report = https://www.uefa.com/uefaeuropaleague/match/2020059/

}}

Spartak Trnava won 6–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 18:00

|team1 = Banants {{fbaicon|ARM}}

|score = 0–1

|team2 = {{fbaicon|CYP}} Omonia

|goals1 =

|goals2 =

• Derbyshire {{goal|26}}

|stadium = Vazgen Sargsyan Republican Stadium, Yerevan{{refn|group=note|name=Banants|Banants played their home match at Vazgen Sargsyan Republican Stadium, Yerevan, instead of their regular stadium Banants Stadium, Yerevan.}}

|attendance = 1,520

|referee = Mario Zebec (Croatia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020008/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:30

|team1 = Omonia {{fbaicon|CYP}}

|score = 4–1

|aet = yes

|team2 = {{fbaicon|ARM}} Banants

|goals1 =

• Roushias {{goal|93||108}}
• Derbyshire {{goal|114}}
• Cleyton {{goal|120+1}}

|goals2 =

• Burayev {{goal|71}}

|stadium = GSP Stadium, Nicosia

|attendance = 8,042

|referee = Aleksandrs Anufrijevs (Latvia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020060/

}}

Omonia won 5–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 21:00

|team1 = Shkëndija {{fbaicon|MKD}}

|score = 2–0

|team2 = {{fbaicon|POL}} Cracovia

|goals1 =

• Ibraimi {{goal|41}}
• Stênio Júnior {{goal|68}}

|goals2 =

|stadium = Philip II Arena, Skopje{{refn|group=note|name=Shkëndija|Shkëndija played their home matches at Philip II Arena, Skopje, instead of their regular stadium City Stadium, Tetovo.}}

|attendance = 4,539

|referee = Sándor Andó-Szabó (Hungary)

|report = https://www.uefa.com/uefaeuropaleague/match/2020009/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 20:00

|team1 = Cracovia {{fbaicon|POL}}

|score = 1–2

|team2 = {{fbaicon|MKD}} Shkëndija

|goals1 =

• Demiri {{goal|68|o.g.}}

|goals2 =

• Ibraimi {{goal|13}}
• Hasani {{goal|90+3}}

|stadium = Józef Piłsudski Cracovia Stadium, Kraków

|attendance = 7,122

|referee = Gunnar Jarl Jónsson (Iceland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020061/

}}

Shkëndija won 4–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 18:30

|team1 = Slavia Sofia {{fbaicon|BUL}}

|score = 1–0

|team2 = {{fbaicon|POL}} Zagłębie Lubin

|goals1 =

• Serderov {{goal|85}}

|goals2 =

|stadium = Vasil Levski National Stadium, Sofia{{refn|group=note|name=Slavia Sofia|Slavia Sofia played their home match at Vasil Levski National Stadium, Sofia, instead of their regular stadium Ovcha Kupel Stadium, Sofia.}}

|attendance = 1,160

|referee = Aliyar Aghayev (Azerbaijan)

|report = https://www.uefa.com/uefaeuropaleague/match/2020010/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:00

|team1 = Zagłębie Lubin {{fbaicon|POL}}

|score = 3–0

|team2 = {{fbaicon|BUL}} Slavia Sofia

|goals1 =

• Guldan {{goal|20}}
• Ł. Piątek {{goal|64}}
• Dąbrowski {{goal|81}}

|goals2 =

|stadium = Stadion Zagłębia Lubin, Lubin

|attendance = 5,817

|referee = Yuriy Mozharovsky (Ukraine)

|report = https://www.uefa.com/uefaeuropaleague/match/2020062/

}}

Zagłębie Lubin won 3–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|30|df=y}}

|time = 16:00

|team1 = Aktobe {{fbaicon|KAZ}}

|score = 1–1

|team2 = {{fbaicon|HUN}} MTK Budapest

|goals1 =

• Zhalmukan {{goal|44|pen.}}

|goals2 =

• Torghelle {{goal|30}}

|stadium = Central Stadium, Aktobe

|attendance = 8,600

|referee = Sascha Amhof (Switzerland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020011/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 18:00

|team1 = MTK Budapest {{fbaicon|HUN}}

|score = 2–0

|team2 = {{fbaicon|KAZ}} Aktobe

|goals1 =

• Nikač {{goal|7}}
• Bese {{goal|84}}

|goals2 =

|stadium = Ménfői út, Győr{{refn|group=note|name=MTK Budapest|MTK Budapest played their home matches at Ménfői út, Győr, instead of their temporary stadium Stadion Rudolf Illovszky, Budapest.}}

|attendance = 601

|referee = Nikolay Yordanov (Bulgaria)

|report = https://www.uefa.com/uefaeuropaleague/match/2020063/

}}

MTK Budapest won 3–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|6|28|df=y}}

|time = 18:00

|team1 = Partizani {{fbaicon|ALB}}

|score = 0–0

|team2 = {{fbaicon|SVK}} Slovan Bratislava

|goals1 =

|goals2 =

|stadium = Elbasan Arena, Elbasan{{refn|group=note|name=Partizani Tirana|Partizani played their first qualifying and play-off rounds home matches at Elbasan Arena, Elbasan, instead of their regular stadium Selman Stërmasi Stadium, Tirana.{{cite web |title=Prvý súťažný zápas novej sezóny odohráme už v utorok |trans-title=The first match of the new season already played on Tuesday |language=sk |url=http://www.skslovan.com/clanok4253-Prvy_sutazny_zapas_novej_sezony_odohrame_uz_v_utorok.htm |website=skslovan.com |publisher=ŠK Slovan Bratislava |date=23 June 2016 |access-date=23 June 2016}}}}

|attendance = 1,350

|referee = Erez Papir (Israel)

|report = https://www.uefa.com/uefaeuropaleague/match/2020012/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 19:00

|team1 = Slovan Bratislava {{fbaicon|SVK}}

|score = Cancelled{{refn|group=note|name=Partizani|Partizani replaced Skënderbeu in the 2016–17 UEFA Champions League second qualifying round and Slovan Bratislava proceeded directly to the UEFA Europa League second qualifying round, after Skënderbeu was excluded by UEFA for match fixing.{{cite web |url=https://www.uefa.com/uefachampionsleague/news/022f-0e9491c5366c-7f36115c125a-1000--partizani-replace-sk%D0%B5nderbeu-in-champions-league/ |title=Partizani replace Skёnderbeu in Champions League |website=UEFA |publisher=Union of European Football Associations |date=6 July 2016 |access-date=6 July 2016}}}}

|team2 = {{fbaicon|ALB}} Partizani

|goals1 =

|goals2 =

|stadium = Štadión FK Senica, Senica{{refn|group=note|name=Slovan Bratislava|Slovan Bratislava would have played their first qualifying round home match at Štadión FK Senica, Senica, instead of their regular stadium Štadión Pasienky, Bratislava.}}

|attendance =

|referee = Mitja Žganec (Slovenia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020064/

}}

Slovan Bratislava won on walkover after Partizani were promoted to the Champions League.{{refn|group=note|name=Partizani}}

----

{{#invoke:football box|main

|date = {{Start date|2016|6|28|df=y}}

|time = 18:00

|team1 = Kapaz {{fbaicon|AZE}}

|score = 0–0

|team2 = {{fbaicon|MDA}} Dacia Chișinău

|goals1 =

|goals2 =

|stadium = Dalga Arena, Baku{{refn|group=note|name=Kapaz|Kapaz played their home matches at Dalga Arena, Baku, instead of their regular stadium City Stadium, Ganja.}}

|attendance = 2,000

|referee = Aleksandr Gauzer (Kazakhstan)

|report = https://www.uefa.com/uefaeuropaleague/match/2020013/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|7|df=y}}

|time = 17:00

|team1 = Dacia Chișinău {{fbaicon|MDA}}

|score = 0–1

|team2 = {{fbaicon|AZE}} Kapaz

|goals1 =

|goals2 =

• Dário {{goal|57}}

|stadium = Stadionul Moldova, Speia

|attendance = 620

|referee = Lasha Silagava (Georgia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020065/

}}

Kapaz won 1–0 on aggregate.

A total of 66 teams played in the second qualifying round: 18 teams which entered in this round, and the 48 winners of the first qualifying round. The draw was held on 20 June 2016. Teams were pre-assigned numbers by UEFA so that the draw could be held in one run for all groups with ten teams and another run for the groups with twelve teams.

class="wikitable" style="font-size:85%"
colspan=2|Group 1 !colspan=2|Group 2 !colspan=2|Group 3
Seeded !Unseeded !Seeded !Unseeded !Seeded !Unseeded
valign=top| {{fbaicon|SRB}} Partizan {{small|(5)}} {{fbaicon|ISR}} Maccabi Haifa {{small|(4)}} {{fbaicon|BLR}} Dinamo Minsk{{Cref2|†|group=1}} {{small|(3)}} {{fbaicon|SRB}} Vojvodina{{Cref2|†|group=1}} {{small|(1)}} {{fbaicon|SVK}} Spartak Trnava{{Cref2|†|group=1}} {{small|(2)}} |valign=top| {{fbaicon|ARM}} Shirak{{Cref2|†|group=1}} {{small|(6)}} {{fbaicon|IRL}} St Patrick's Athletic{{Cref2|†|group=1}} {{small|(10)}} {{fbaicon|POL}} Zagłębie Lubin{{Cref2|†|group=1}} {{small|(7)}} {{fbaicon|WAL}} Connah's Quay Nomads{{Cref2|†|group=1}} {{small|(8)}} {{fbaicon|EST}} Nõmme Kalju{{Cref2|†|group=1}} {{small|(9)}} |valign=top| {{fbaicon|AUT}} Austria Wien {{small|(5)}} {{fbaicon|FIN}} HJK{{Cref2|†|group=1}} {{small|(4)}} {{fbaicon|HUN}} MTK Budapest{{Cref2|†|group=1}} {{small|(1)}} {{fbaicon|BLR}} Shakhtyor Soligorsk{{Cref2|†|group=1}} {{small|(3)}} {{fbaicon|DEN}} Brøndby{{Cref2|†|group=1}} {{small|(2)}} |valign=top| {{fbaicon|AZE}} Gabala{{Cref2|†|group=1}} {{small|(8)}} {{fbaicon|ALB}} Kukësi{{Cref2|†|group=1}} {{small|(7)}} {{fbaicon|SCO}} Hibernian {{small|(6)}} {{fbaicon|BUL}} Beroe Stara Zagora{{Cref2|†|group=1}} {{small|(9)}} {{fbaicon|SVN}} Domžale{{Cref2|†|group=1}} {{small|(10)}} |valign=top| {{fbaicon|DEN}} Midtjylland{{Cref2|†|group=1}} {{small|(1)}} {{fbaicon|SUI}} Grasshopper {{small|(5)}} {{fbaicon|AZE}} Neftçi{{Cref2|†|group=1}} {{small|(3)}} {{fbaicon|TUR}} Osmanlıspor {{small|(4)}} {{fbaicon|CRO}} Lokomotiva Zagreb{{Cref2|†|group=1}} {{small|(2)}} |valign=top| {{fbaicon|ISL}} KR{{Cref2|†|group=1}} {{small|(7)}} {{fbaicon|LIE}} Vaduz{{Cref2|†|group=1}} {{small|(8)}} {{fbaicon|FIN}} RoPS{{Cref2|†|group=1}} {{small|(6)}} {{fbaicon|MKD}} Shkëndija{{Cref2|†|group=1}} {{small|(10)}} {{fbaicon|MDA}} Zimbru Chișinău{{Cref2|†|group=1}} {{small|(9)}}
colspan=2|Group 4 !colspan=2|Group 5 !colspan=2|Group 6
Seeded !Unseeded !Seeded !Unseeded !Seeded !Unseeded
valign=top| {{fbaicon|SVN}} Maribor {{small|(6)}} {{fbaicon|CYP}} Omonia{{Cref2|†|group=1}} {{small|(5)}} {{fbaicon|SVK}} Slovan Bratislava{{Cref2|†|group=1}} {{small|(3)}} {{fbaicon|SWE}} IFK Göteborg{{Cref2|†|group=1}} {{small|(4)}} {{fbaicon|SCO}} Heart of Midlothian{{Cref2|†|group=1}} {{small|(2)}} {{fbaicon|GRE}} PAS Giannina {{small|(1)}} |valign=top| {{fbaicon|NOR}} Odd{{Cref2|†|group=1}} {{small|(7)}} {{fbaicon|POL}} Piast Gliwice {{small|(9)}} {{fbaicon|BUL}} Levski Sofia {{small|(11)}} {{fbaicon|ISR}} Beitar Jerusalem{{Cref2|†|group=1}} {{small|(10)}} {{fbaicon|LVA}} Jelgava{{Cref2|†|group=1}} {{small|(8)}} {{fbaicon|MLT}} Birkirkara{{Cref2|†|group=1}} {{small|(12)}} |valign=top| {{fbaicon|ISR}} Maccabi Tel Aviv{{Cref2|†|group=1}} {{small|(4)}} {{fbaicon|CRO}} Hajduk Split {{small|(5)}} {{fbaicon|HUN}} Debrecen{{Cref2|†|group=1}} {{small|(3)}} {{fbaicon|AUT}} Admira Wacker Mödling{{Cref2|†|group=1}} {{small|(1)}} {{fbaicon|LVA}} Ventspils{{Cref2|†|group=1}} {{small|(2)}} {{fbaicon|SWE}} BK Häcken {{small|(6)}} |valign=top| {{fbaicon|SCO}} Aberdeen{{Cref2|†|group=1}} {{small|(12)}} {{fbaicon|ROU}} CSM Politehnica Iași {{small|(10)}} {{fbaicon|KAZ}} Kairat{{Cref2|†|group=1}} {{small|(9)}} {{fbaicon|IRL}} Cork City{{Cref2|†|group=1}} {{small|(11)}} {{fbaicon|AZE}} Kapaz{{Cref2|†|group=1}} {{small|(7)}} {{fbaicon|BLR}} Torpedo-BelAZ Zhodino {{small|(8)}} |valign=top| {{fbaicon|BEL}} Genk {{small|(3)}} {{fbaicon|CYP}} AEK Larnaca{{Cref2|†|group=1}} {{small|(2)}} {{fbaicon|SWE}} AIK{{Cref2|†|group=1}} {{small|(6)}} {{fbaicon|HUN}} Videoton{{Cref2|†|group=1}} {{small|(1)}} {{fbaicon|NOR}} Strømsgodset {{small|(5)}} {{fbaicon|CZE}} Slavia Prague {{small|(4)}} |valign=top| {{fbaicon|MNE}} Budućnost Podgorica{{Cref2|†|group=1}} {{small|(8)}} {{fbaicon|NIR}} Cliftonville{{Cref2|†|group=1}} {{small|(12)}} {{fbaicon|SRB}} Čukarički{{Cref2|†|group=1}} {{small|(7)}} {{fbaicon|EST}} Levadia Tallinn{{Cref2|†|group=1}} {{small|(9)}} {{fbaicon|GIB}} Europa{{Cref2|†|group=1}} {{small|(11)}} {{fbaicon|DEN}} SønderjyskE {{small|(10)}}

;Notes

{{Cnote2 Begin|liststyle=disc}}

{{Cnote2|†|n=0|group=1|^† Winners of the first qualifying round whose identity was not known at the time of the draw. Teams in italics defeated a team with a higher coefficient in the first qualifying round, thus effectively taking the coefficient of their defeated opponent in the draw for the second qualifying round.}}

{{Cnote2 End}}

The first legs were played on 14 July, and the second legs were played on 20 and 21 July 2016.

{{#invoke:Sports series|main|generate_links=y

|Shirak|ARM|1–3|Spartak Trnava|SVK|1–1|0–2

|Dinamo Minsk|BLR|2–1|St Patrick's Athletic|IRL|1–1|1–0

|Partizan|SRB|0–0 (3–4 p)|Zagłębie Lubin|POL|0–0|0–0 (aet)

|Vojvodina|SRB|3–1|Connah's Quay Nomads|WAL|1–0|2–1

|Maccabi Haifa|ISR|2–2 (3–5 p)|Nõmme Kalju|EST|1–1|1–1 (aet)

|Hibernian|SCO|1–1 (3–5 p)|Brøndby|DEN|0–1|1–0 (aet)

|Shakhtyor Soligorsk|BLR|2–3|Domžale|SVN|1–1|1–2

|Austria Wien|AUT|5–1|Kukësi|ALB|1–0|4–1

|MTK Budapest|HUN|1–4|Gabala|AZE|1–2|0–2

|Beroe Stara Zagora|BUL|1–2|HJK|FIN|1–1|0–1

|RoPS|FIN|1–4|Lokomotiva Zagreb|CRO|1–1|0–3

|Neftçi|AZE|0–1|Shkëndija|MKD|0–0|0–1

|KR|ISL|4–5|Grasshopper|SUI|3–3|1–2

|Midtjylland|DEN|5–2|Vaduz|LIE|3–0|2–2

|Zimbru Chișinău|MDA|2–7|Osmanlıspor|TUR|2–2|0–5

|PAS Giannina|GRE|4–3|Odd|NOR|3–0|1–3 (aet)

|Birkirkara|MLT|2–1|Heart of Midlothian|SCO|0–0|2–1

|Maribor|SVN|1–1 (a)|Levski Sofia|BUL|0–0|1–1

|Piast Gliwice|POL|0–3|IFK Göteborg|SWE|0–3|0–0

|Slovan Bratislava|SVK|0–3|Jelgava|LVA|0–0|0–3

|Beitar Jerusalem|ISR|3–3 (a)|Omonia|CYP|1–0|2–3

|Admira Wacker Mödling|AUT|3–0|Kapaz|AZE|1–0|2–0

|Aberdeen|SCO|4–0|Ventspils|LVA|3–0|1–0

|BK Häcken|SWE|1–2|Cork City|IRL|1–1|0–1

|Kairat|KAZ|2–3|Maccabi Tel Aviv|ISR|1–1|1–2

|Debrecen|HUN|1–3|Torpedo-BelAZ Zhodino|BLR|1–2|0–1

|CSM Politehnica Iași|ROU|3–4|Hajduk Split|CRO|2–2|1–2

|Videoton|HUN|3–1|Čukarički|SRB|2–0|1–1

|Cliftonville|NIR|2–5|AEK Larnaca|CYP|2–3|0–2

|AIK|SWE|2–0|Europa|GIB|1–0|1–0

|Levadia Tallinn|EST|3–3 (a)|Slavia Prague|CZE|3–1|0–2

|Genk|BEL|2–2 (4–2 p)|Budućnost Podgorica|MNE|2–0|0–2 (aet)

|SønderjyskE|DEN|4–3|Strømsgodset|NOR|2–1|2–2 (aet)

|note_agg_5=Order of legs reversed after original draw.

|note_agg_13=agg_5

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 15:00

|team1 = Shirak {{fbaicon|ARM}}

|score = 1–1

|team2 = {{fbaicon|SVK}} Spartak Trnava

|goals1 =

• Hakobyan {{goal|16}}

|goals2 =

• Jirka {{goal|87}}

|stadium = City Stadium, Gyumri

|attendance = 2,747{{cite web |title=Summary UEFA Europa League - Round 2 |url=https://int.soccerway.com/international/europe/uefa-cup/20162017/2nd-qualifying-round/r35524/ |publisher=Soccerway |access-date=17 July 2016}}

|referee = Artyom Kuchin (Kazakhstan)

|report = https://www.uefa.com/uefaeuropaleague/match/2020070/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 20:15

|team1 = Spartak Trnava {{fbaicon|SVK}}

|score = 2–0

|team2 = {{fbaicon|ARM}} Shirak

|goals1 =

• Schranz {{goal|57}}
• Tambe {{goal|61}}

|goals2 =

|stadium = Štadión Antona Malatinského, Trnava

|attendance = 6,129

|referee = Arnold Hunter (Northern Ireland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020110/

}}

Spartak Trnava won 3–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 17:30

|team1 = Dinamo Minsk {{fbaicon|BLR}}

|score = 1–1

|team2 = {{fbaicon|IRL}} St Patrick's Athletic

|goals1 =

• Karytska {{goal|25}}

|goals2 =

• Fagan {{goal|54}}

|stadium = Traktor Stadium, Minsk

|attendance = 1,286

|referee = Srđan Jovanović (Serbia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020071/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 20:45

|team1 = St Patrick's Athletic {{fbaicon|IRL}}

|score = 0–1

|team2 = {{fbaicon|BLR}} Dinamo Minsk

|goals1 =

|goals2 =

• Rassadkin {{goal|18}}

|stadium = Richmond Park, Dublin

|attendance = 2,400

|referee = Alan Mario Sant (Malta)

|report = https://www.uefa.com/uefaeuropaleague/match/2020111/

}}

Dinamo Minsk won 2–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 20:15

|team1 = Partizan {{fbaicon|SRB}}

|score = 0–0

|team2 = {{fbaicon|POL}} Zagłębie Lubin

|goals1 =

|goals2 =

|stadium = Partizan Stadium, Belgrade

|attendance = 15,870

|referee = Eitan Shemeulevitch (Israel)

|report = https://www.uefa.com/uefaeuropaleague/match/2020072/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 21:05

|team1 = Zagłębie Lubin {{fbaicon|POL}}

|score = 0–0

|aet = yes

|team2 = {{fbaicon|SRB}} Partizan

|goals1 =

|goals2 =

|stadium = Stadion Zagłębia Lubin, Lubin

|attendance = 11,279

|referee = Anatoliy Abdula (Ukraine)

|penalties1 =

• Janus {{pengoal}}
• Guldan {{pengoal}}
• Todorovski {{penmiss}}
• Woźniak {{pengoal}}
• Vlasko {{pengoal}}

|penaltyscore = 4–3

|penalties2 =

• {{penmiss}} Brašanac
• {{pengoal}} Ilić
• {{pengoal}} Đuričković
• {{pengoal}} Janković
• {{penmiss}} Mihajlović

|report = https://www.uefa.com/uefaeuropaleague/match/2020112/

}}

0–0 on aggregate; Zagłębie Lubin won 4–3 on penalties.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 20:00

|team1 = Vojvodina {{fbaicon|SRB}}

|score = 1–0

|team2 = {{fbaicon|WAL}} Connah's Quay Nomads

|goals1 =

• Paločević {{goal|86}}

|goals2 =

|stadium = Karađorđe Stadium, Novi Sad

|attendance = 4,276

|referee = Aleksei Nikolaev (Russia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020073/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 19:45

|team1 = Connah's Quay Nomads {{fbaicon|WAL}}

|score = 1–2

|team2 = {{fbaicon|SRB}} Vojvodina

|goals1 =

• Wilde {{goal|65}}

|goals2 =

• Meleg {{goal|8||49|pen.}}

|stadium = Belle Vue, Rhyl{{refn|group=note|name=Connah's Quay Nomads}}

|attendance = 809

|referee = Peter Kralović (Slovakia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020113/

}}

Vojvodina won 3–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 19:00

|team1 = Maccabi Haifa {{fbaicon|ISR}}

|score = 1–1

|team2 = {{fbaicon|EST}} Nõmme Kalju

|goals1 =

• Vermouth {{goal|70}}

|goals2 =

• Toomet {{goal|47}}

|stadium = Netanya Stadium, Netanya{{refn|group=note|name=Maccabi Haifa|Maccabi Haifa played their home match at Netanya Stadium, Netanya, instead of their regular stadium Sammy Ofer Stadium, Haifa.{{cite web |title="סמי עופר יהיה מוכן לפתיחת הליגה" |trans-title=Sammy Ofer will be ready for league opening |language=he |url=http://mhaifafc.com/newsPage.asp?newsID=25266 |website=mhaifafc.com |publisher=Maccabi Haifa F.C. |date=28 June 2016 |access-date=1 July 2016}}}}

|attendance = 6,500

|referee = Svein-Erik Edvartsen (Norway)

|report = https://www.uefa.com/uefaeuropaleague/match/2020074/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 18:00

|team1 = Nõmme Kalju {{fbaicon|EST}}

|score = 1–1

|aet = yes

|team2 = {{fbaicon|ISR}} Maccabi Haifa

|goals1 =

• Neemelo {{goal|90}}

|goals2 =

• Rukavytsya {{goal|34|pen.}}

|stadium = Kadriorg Stadium, Tallinn{{refn|group=note|name=Nõmme Kalju}}

|attendance = 2,273

|referee = Markus Hameter (Austria)

|penalties1 =

• Uggè {{pengoal}}
• Sidorenkov {{pengoal}}
• Purje {{pengoal}}
• Wakui {{pengoal}}
• Subbotin {{pengoal}}

|penaltyscore = 5–3

|penalties2 =

• {{pengoal}} Obraniak
• {{pengoal}} Rukavytsya
• {{penmiss}} Zenati
• {{pengoal}} Menachem

|report = https://www.uefa.com/uefaeuropaleague/match/2020114/

}}

2–2 on aggregate; Nõmme Kalju won 5–3 on penalties.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 20:45

|team1 = Hibernian {{fbaicon|SCO}}

|score = 0–1

|team2 = {{fbaicon|DEN}} Brøndby

|goals1 =

|goals2 =

• Wilczek {{goal|1}}

|stadium = Easter Road, Edinburgh

|attendance = 13,454

|referee = Juan Martínez Munuera (Spain)

|report = https://www.uefa.com/uefaeuropaleague/match/2020075/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 20:00

|team1 = Brøndby {{fbaicon|DEN}}

|score = 0–1

|aet = yes

|team2 = {{fbaicon|SCO}} Hibernian

|goals1 =

|goals2 =

• Gray {{goal|62}}

|stadium = Brøndby Stadium, Brøndbyvester

|attendance = 11,548

|referee = Marius Avram (Romania)

|penalties1 =

• Larsson {{pengoal}}
• Nørgaard {{pengoal}}
• Stückler {{pengoal}}
• Wilczek {{pengoal}}
• Holst {{pengoal}}

|penaltyscore = 5–3

|penalties2 =

• {{penmiss}} McGinn
• {{pengoal}} Hanlon
• {{pengoal}} Holt
• {{pengoal}} Boyle

|report = https://www.uefa.com/uefaeuropaleague/match/2020115/

}}

1–1 on aggregate; Brøndby won 5–3 on penalties.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 19:30

|team1 = Shakhtyor Soligorsk {{fbaicon|BLR}}

|score = 1–1

|team2 = {{fbaicon|SVN}} Domžale

|goals1 =

• Ignjatijević {{goal|35}}

|goals2 =

• Trajkovski {{goal|52}}

|stadium = Stroitel Stadium, Salihorsk

|attendance = 2,100

|referee = Dumitru Muntean (Moldova)

|report = https://www.uefa.com/uefaeuropaleague/match/2020076/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 20:30

|team1 = Domžale {{fbaicon|SVN}}

|score = 2–1

|team2 = {{fbaicon|BLR}} Shakhtyor Soligorsk

|goals1 =

• Alvir {{goal|35}}
• Majer {{goal|69}}

|goals2 =

• Laptsew {{goal|61}}

|stadium = Sports Park, Domžale

|attendance = 1,800

|referee = Alain Bieri (Switzerland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020116/

}}

Domžale won 3–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 21:05

|team1 = Austria Wien {{fbaicon|AUT}}

|score = 1–0

|team2 = {{fbaicon|ALB}} Kukësi

|goals1 =

• Pires {{goal|24}}

|goals2 =

|stadium = Ernst-Happel-Stadion, Vienna{{refn|group=note|name=Austria Wien|Austria Wien played their home matches at Ernst-Happel-Stadion, Vienna, instead of their regular stadium Franz Horr Stadium, Vienna, due to reconstruction.{{cite web |title=Austria startet Crowd-Investing-Kampagne für Stadion |trans-title=Austria launched crowd-investing campaign for stadium |language=de |url=http://www.stadionwelt.de/sw_stadien/index.php?head=Austria-startet-Crowd-Investing-Kampagne-fuer-Stadion&folder=sites&site=news_detail&news_id=14227 |website=stadionwelt.de |publisher=Stadiowelt Inside |date=18 May 2016 |access-date=8 July 2016 |archive-date=12 June 2018 |archive-url=https://web.archive.org/web/20180612211347/https://www.stadionwelt.de/sw_stadien/index.php?head=Austria-startet-Crowd-Investing-Kampagne-fuer-Stadion&folder=sites&site=news_detail&news_id=14227 |url-status=dead }}}}

|attendance = 4,312

|referee = Paolo Valeri (Italy)

|report = https://www.uefa.com/uefaeuropaleague/match/2020077/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 19:30

|team1 = Kukësi {{fbaicon|ALB}}

|score = 1–4

|team2 = {{fbaicon|AUT}} Austria Wien

|goals1 =

• Hallaçi {{goal|78}}

|goals2 =

• Kayode {{goal|16||58}}
• Holzhauser {{goal|67}}
• Martschinko {{goal|90+4}}

|stadium = Elbasan Arena, Elbasan{{refn|group=note|name=Kukësi}}

|attendance = 1,580

|referee = Vilhjálmur Alvar Þórarinsson (Iceland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020117/

}}

Austria Wien won 5–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 20:30

|team1 = MTK Budapest {{fbaicon|HUN}}

|score = 1–2

|team2 = {{fbaicon|AZE}} Gabala

|goals1 =

• Torghelle {{goal|70}}

|goals2 =

• Kvekveskiri {{goal|25}}
• Ozobić {{goal|63}}

|stadium = Ménfői út, Győr{{refn|group=note|name=MTK Budapest}}

|attendance = 501

|referee = Bojan Pandžić (Sweden)

|report = https://www.uefa.com/uefaeuropaleague/match/2020078/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 19:00

|team1 = Gabala {{fbaicon|AZE}}

|score = 2–0

|team2 = {{fbaicon|HUN}} MTK Budapest

|goals1 =

• Zenjov {{goal|7}}
• Weeks {{goal|37}}

|goals2 =

|stadium = Bakcell Arena, Baku{{refn|group=note|name=Gabala}}

|attendance = 5,550

|referee = Mete Kalkavan (Turkey)

|report = https://www.uefa.com/uefaeuropaleague/match/2020118/

}}

Gabala won 4–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 19:30

|team1 = Beroe Stara Zagora {{fbaicon|BUL}}

|score = 1–1

|team2 = {{fbaicon|FIN}} HJK

|goals1 =

• Penev {{goal|49}}

|goals2 =

• Morelos {{goal|38}}

|stadium = Beroe Stadium, Stara Zagora

|attendance = 4,424

|referee = Petr Ardeleanu (Czech Republic)

|report = https://www.uefa.com/uefaeuropaleague/match/2020079/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 18:00

|team1 = HJK {{fbaicon|FIN}}

|score = 1–0

|team2 = {{fbaicon|BUL}} Beroe Stara Zagora

|goals1 =

• Tanaka {{goal|25}}

|goals2 =

|stadium = Sonera Stadium, Helsinki

|attendance = 3,872

|referee = Padraig Sutton (Republic of Ireland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020119/

}}

HJK won 2–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 18:00

|team1 = RoPS {{fbaicon|FIN}}

|score = 1–1

|team2 = {{fbaicon|CRO}} Lokomotiva Zagreb

|goals1 =

• Prenga {{goal|87|o.g.}}

|goals2 =

• Jammeh {{goal|73|o.g.}}

|stadium = Keskuskenttä, Rovaniemi

|attendance = 1,812

|referee = Þorvaldur Árnason (Iceland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020080/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 18:00

|team1 = Lokomotiva Zagreb {{fbaicon|CRO}}

|score = 3–0

|team2 = {{fbaicon|FIN}} RoPS

|goals1 =

• Fiolić {{goal|44}}
• Marić {{goal|49||83}}

|goals2 =

|stadium = Stadion Kranjčevićeva, Zagreb

|attendance = 630

|referee = Giorgi Kruashvili (Georgia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020120/

}}

Lokomotiva Zagreb won 4–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 18:00

|team1 = Neftçi {{fbaicon|AZE}}

|score = 0–0

|team2 = {{fbaicon|MKD}} Shkëndija

|goals1 =

|goals2 =

|stadium = Bakcell Arena, Baku

|attendance = 6,891

|referee = Sergey Tsinkevich (Belarus)

|report = https://www.uefa.com/uefaeuropaleague/match/2020081/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 20:00

|team1 = Shkëndija {{fbaicon|MKD}}

|score = 1–0

|team2 = {{fbaicon|AZE}} Neftçi

|goals1 =

• Ibraimi {{goal|31}}

|goals2 =

|stadium = Philip II Arena, Skopje{{refn|group=note|name=Shkëndija}}

|attendance = 9,510

|referee = Erik Lambrechts (Belgium)

|report = https://www.uefa.com/uefaeuropaleague/match/2020121/

}}

Shkëndija won 1–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 21:15

|team1 = KR {{fbaicon|ISL}}

|score = 3–3

|team2 = {{fbaicon|SUI}} Grasshopper

|goals1 =

• Andersen {{goal|46||50}}
• Hauksson {{goal|77|pen.}}

|goals2 =

• Munsy {{goal|18}}
• Gjorgjev {{goal|36}}
• Caio {{goal|59}}

|stadium = KR-völlur, Reykjavík

|attendance = 767

|referee = Peter Kjærsgaard-Andersen (Denmark)

|report = https://www.uefa.com/uefaeuropaleague/match/2020082/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 19:00

|team1 = Grasshopper {{fbaicon|SUI}}

|score = 2–1

|team2 = {{fbaicon|ISL}} KR

|goals1 =

• Sigurjónsson {{goal|45||68}}

|goals2 =

• Andersen {{goal|52}}

|stadium = Letzigrund, Zürich

|attendance = 3,940

|referee = Erez Papir (Israel)

|report = https://www.uefa.com/uefaeuropaleague/match/2020122/

}}

Grasshopper won 5–4 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 18:30

|team1 = Midtjylland {{fbaicon|DEN}}

|score = 3–0

|team2 = {{fbaicon|LIE}} Vaduz

|goals1 =

• Sisto {{goal|20||82}}
• Onuachu {{goal|73}}

|goals2 =

|stadium = MCH Arena, Herning

|attendance = 4,455

|referee = Kirill Levnikov (Russia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020083/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 19:00

|team1 = Vaduz {{fbaicon|LIE}}

|score = 2–2

|team2 = {{fbaicon|DEN}} Midtjylland

|goals1 =

• Brunner {{goal|83}}
• Costanzo {{goal|86|pen.}}

|goals2 =

• Sisto {{goal|41||68}}

|stadium = Rheinpark Stadion, Vaduz

|attendance = 842

|referee = Andrew Davey (Northern Ireland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020123/

}}

Midtjylland won 5–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 19:00

|team1 = Zimbru Chișinău {{fbaicon|MDA}}

|score = 2–2

|team2 = {{fbaicon|TUR}} Osmanlıspor

|goals1 =

• Zagaevschi {{goal|24}}
• Damașcan {{goal|62}}

|goals2 =

• Çürüksu {{goal|12}}
• Bekdemir {{goal|77}}

|stadium = Zimbru Stadium, Chișinău

|attendance = 4,160

|referee = Nenad Đokić (Serbia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020084/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 20:00

|team1 = Osmanlıspor {{fbaicon|TUR}}

|score = 5–0

|team2 = {{fbaicon|MDA}} Zimbru Chișinău

|goals1 =

• Umar {{goal|16|pen.|26||50}}
• Kılıçaslan {{goal|74}}
• Rusescu {{goal|83}}

|goals2 =

|stadium = Osmanlı Stadyumu, Ankara

|attendance = 6,382

|referee = Mitja Žganec (Slovenia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020124/

}}

Osmanlıspor won 7–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 20:00

|team1 = PAS Giannina {{fbaicon|GRE}}

|score = 3–0

|team2 = {{fbaicon|NOR}} Odd

|goals1 =

• Michail {{goal|7}}
• Fonsi {{goal|31}}
• Acosta {{goal|68}}

|goals2 =

|stadium = Zosimades Stadium, Ioannina

|attendance = 5,615

|referee = Glenn Nyberg (Sweden)

|report = https://www.uefa.com/uefaeuropaleague/match/2020085/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 19:00

|team1 = Odd {{fbaicon|NOR}}

|score = 3–1

|aet = yes

|team2 = {{fbaicon|GRE}} PAS Giannina

|goals1 =

• Nordkvelle {{goal|55|pen.}}
• Bentley {{goal|57}}
• Ruud {{goal|89}}

|goals2 =

• Koutris {{goal|98}}

|stadium = Skagerak Arena, Skien

|attendance = 3,184

|referee = Tomasz Musiał (Poland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020125/

}}

PAS Giannina won 4–3 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 20:30

|team1 = Birkirkara {{fbaicon|MLT}}

|score = 0–0

|team2 = {{fbaicon|SCO}} Heart of Midlothian

|goals1 =

|goals2 =

|stadium = Hibernians Stadium, Paola{{refn|group=note|name=Birkirkara}}

|attendance = 1,868

|referee = Ivaylo Stoyanov (Bulgaria)

|report = https://www.uefa.com/uefaeuropaleague/match/2020086/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 21:00

|team1 = Heart of Midlothian {{fbaicon|SCO}}

|score = 1–2

|team2 = {{fbaicon|MLT}} Birkirkara

|goals1 =

• Sammon {{goal|74}}

|goals2 =

• Bubalović {{goal|55}}
• Herrera {{goal|67}}

|stadium = Tynecastle Stadium, Edinburgh

|attendance = 14,301

|referee = Ville Nevalainen (Finland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020126/

}}

Birkirkara won 2–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 20:00

|team1 = Maribor {{fbaicon|SVN}}

|score = 0–0

|team2 = {{fbaicon|BUL}} Levski Sofia

|goals1 =

|goals2 =

|stadium = Ljudski vrt, Maribor

|attendance = 7,345

|referee = Cristian Balaj (Romania)

|report = https://www.uefa.com/uefaeuropaleague/match/2020087/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 19:00

|team1 = Levski Sofia {{fbaicon|BUL}}

|score = 1–1

|team2 = {{fbaicon|SVN}} Maribor

|goals1 =

• Narh {{goal|22}}

|goals2 =

• Tavares {{goal|68}}

|stadium = Georgi Asparuhov Stadium, Sofia

|attendance = 17,600

|referee = Michael Tykgaard (Denmark)

|report = https://www.uefa.com/uefaeuropaleague/match/2020127/

}}

1–1 on aggregate; Maribor won on away goals.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 20:45

|team1 = Piast Gliwice {{fbaicon|POL}}

|score = 0–3

|team2 = {{fbaicon|SWE}} IFK Göteborg

|goals1 =

|goals2 =

• Rogne {{goal|2}}
• Hysén {{goal|35}}
• Engvall {{goal|86}}

|stadium = Stadion Piast, Gliwice

|attendance = 5,629

|referee = Manuel Schüttengruber (Austria)

|report = https://www.uefa.com/uefaeuropaleague/match/2020088/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 19:00

|team1 = IFK Göteborg {{fbaicon|SWE}}

|score = 0–0

|team2 = {{fbaicon|POL}} Piast Gliwice

|goals1 =

|goals2 =

|stadium = Gamla Ullevi, Gothenburg

|attendance = 7,276

|referee = Georgios Kominis (Greece)

|report = https://www.uefa.com/uefaeuropaleague/match/2020128/

}}

IFK Göteborg won 3–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 20:15

|team1 = Slovan Bratislava {{fbaicon|SVK}}

|score = 0–0

|team2 = {{fbaicon|LVA}} Jelgava

|goals1 =

|goals2 =

|stadium = Štadión Pasienky, Bratislava

|attendance = 1,451

|referee = Alexandros Aretopoulos (Greece)

|report = https://www.uefa.com/uefaeuropaleague/match/2020089/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 17:30

|team1 = Jelgava {{fbaicon|LVA}}

|score = 3–0

|team2 = {{fbaicon|SVK}} Slovan Bratislava

|goals1 =

• Kļuškins {{goal|27|pen.}}
• Bogdaškins {{goal|48}}
• Malašenoks {{goal|85}}

|goals2 =

|stadium = Olympic Sports Center of Zemgale, Jelgava

|attendance = 1,560

|referee = Ken Henry Johnsen (Norway)

|report = https://www.uefa.com/uefaeuropaleague/match/2020129/

}}

Jelgava won 3–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 19:00

|team1 = Beitar Jerusalem {{fbaicon|ISR}}

|score = 1–0

|team2 = {{fbaicon|CYP}} Omonia

|goals1 =

• Abuhatzira {{goal|71}}

|goals2 =

|stadium = Teddy Stadium, Jerusalem

|attendance = 9,200

|referee = Marcin Borski (Poland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020090/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 18:30

|team1 = Omonia {{fbaicon|CYP}}

|score = 3–2

|team2 = {{fbaicon|ISR}} Beitar Jerusalem

|goals1 =

• Agayev {{goal|26}}
• Sheridan {{goal|45+3|pen.}}
• Roushias {{goal|81}}

|goals2 =

• Atzili {{goal|17||45|pen.}}

|stadium = GSP Stadium, Nicosia

|attendance = 14,383

|referee = Davide Massa (Italy)

|report = https://www.uefa.com/uefaeuropaleague/match/2020130/

}}

3–3 on aggregate; Beitar Jerusalem won on away goals.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 19:00

|team1 = Admira Wacker Mödling {{fbaicon|AUT}}

|score = 1–0

|team2 = {{fbaicon|AZE}} Kapaz

|goals1 =

• Starkl {{goal|41}}

|goals2 =

|stadium = NV Arena, Sankt Pölten{{refn|group=note|name=Admira Wacker Mödling}}

|attendance = 956

|referee = Pavle Radovanović (Montenegro)

|report = https://www.uefa.com/uefaeuropaleague/match/2020091/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|20|df=y}}

|time = 18:00

|team1 = Kapaz {{fbaicon|AZE}}

|score = 0–2

|team2 = {{fbaicon|AUT}} Admira Wacker Mödling

|goals1 =

|goals2 =

• Knasmüllner {{goal|17}}
• Schmidt {{goal|76}}

|stadium = Dalga Arena, Baku{{refn|group=note|name=Kapaz}}

|attendance = 1,650

|referee = Vitali Meshkov (Russia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020131/

}}

Admira Wacker Mödling won 3–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 20:45

|team1 = Aberdeen {{fbaicon|SCO}}

|score = 3–0

|team2 = {{fbaicon|LVA}} Ventspils

|goals1 =

• Stockley {{goal|72}}
• Rooney {{goal|76}}
• Burns {{goal|90+2}}

|goals2 =

|stadium = Pittodrie Stadium, Aberdeen

|attendance = 10,672

|referee = João Pinheiro (Portugal)

|report = https://www.uefa.com/uefaeuropaleague/match/2020092/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 17:00

|team1 = Ventspils {{fbaicon|LVA}}

|score = 0–1

|team2 = {{fbaicon|SCO}} Aberdeen

|goals1 =

|goals2 =

• Rooney {{goal|79}}

|stadium = Olimpiskais Stadions, Ventspils

|attendance = 2,100

|referee = Danilo Grujić (Serbia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020132/

}}

Aberdeen won 4–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 19:00

|team1 = BK Häcken {{fbaicon|SWE}}

|score = 1–1

|team2 = {{fbaicon|IRL}} Cork City

|goals1 =

• Owoeri {{goal|83}}

|goals2 =

• Maguire {{goal|64|pen.}}

|stadium = Bravida Arena, Gothenburg

|attendance = 2,022

|referee = Amaury Delerue (France)

|report = https://www.uefa.com/uefaeuropaleague/match/2020093/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 20:45

|team1 = Cork City {{fbaicon|IRL}}

|score = 1–0

|team2 = {{fbaicon|SWE}} BK Häcken

|goals1 =

• O'Connor {{goal|26}}

|goals2 =

|stadium = Turners Cross, Cork

|attendance = 5,334

|referee = Carlos Xistra (Portugal)

|report = https://www.uefa.com/uefaeuropaleague/match/2020133/

}}

Cork City won 2–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 16:45

|team1 = Kairat {{fbaicon|KAZ}}

|score = 1–1

|team2 = {{fbaicon|ISR}} Maccabi Tel Aviv

|goals1 =

• Arshavin {{goal|29}}

|goals2 =

• Benayoun {{goal|90+1}}

|stadium = Central Stadium, Almaty

|attendance = 22,500

|referee = Antti Munukka (Finland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020094/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 19:00

|team1 = Maccabi Tel Aviv {{fbaicon|ISR}}

|score = 2–1

|team2 = {{fbaicon|KAZ}} Kairat

|goals1 =

• Ben Haim II {{goal|5}}
• Alberman {{goal|86}}

|goals2 =

• Gohou {{goal|64}}

|stadium = Netanya Stadium, Netanya{{refn|group=note|name=Maccabi Tel Aviv}}

|attendance = 9,832

|referee = Tiago Martins (Portugal)

|report = https://www.uefa.com/uefaeuropaleague/match/2020134/

}}

Maccabi Tel Aviv won 3–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 18:30

|team1 = Debrecen {{fbaicon|HUN}}

|score = 1–2

|team2 = {{fbaicon|BLR}} Torpedo-BelAZ Zhodino

|goals1 =

• Tisza {{goal|2}}

|goals2 =

• Zahynaylov {{goal|23}}
• Klopotskiy {{goal|88}}

|stadium = Nagyerdei Stadion, Debrecen

|attendance = 6,015

|referee = Leontios Trattou (Cyprus)

|report = https://www.uefa.com/uefaeuropaleague/match/2020095/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 18:00

|team1 = Torpedo-BelAZ Zhodino {{fbaicon|BLR}}

|score = 1–0

|team2 = {{fbaicon|HUN}} Debrecen

|goals1 =

• Dzemidovich {{goal|25}}

|goals2 =

|stadium = Torpedo Stadium, Zhodzina

|attendance = 2,650

|referee = Dimitar Meckarovski (Macedonia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020135/

}}

Torpedo-BelAZ Zhodino won 3–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 20:00

|team1 = CSM Politehnica Iași {{fbaicon|ROU}}

|score = 2–2

|team2 = {{fbaicon|CRO}} Hajduk Split

|goals1 =

• Cristea {{goal|19}}
• Piccioni {{goal|23}}

|goals2 =

• Ohandza {{goal|48}}
• Said {{goal|90+4}}

|stadium = Stadionul Emil Alexandrescu, Iași

|attendance = 8,004

|referee = Yuriy Mozharovsky (Ukraine)

|report = https://www.uefa.com/uefaeuropaleague/match/2020096/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 20:30

|team1 = Hajduk Split {{fbaicon|CRO}}

|score = 2–1

|team2 = {{fbaicon|ROU}} CSM Politehnica Iași

|goals1 =

• Tudor {{goal|22}}
• Ohandza {{goal|90}}

|goals2 =

• Ciucur {{goal|26}}

|stadium = Stadion Poljud, Split

|attendance = 16,798

|referee = Frank Schneider (France)

|report = https://www.uefa.com/uefaeuropaleague/match/2020136/

}}

Hajduk Split won 4–3 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 20:30

|team1 = Videoton {{fbaicon|HUN}}

|score = 2–0

|team2 = {{fbaicon|SRB}} Čukarički

|goals1 =

• Bódi {{goal|58}}
• Suljić {{goal|90+2}}

|goals2 =

|stadium = Pancho Arena, Felcsút{{refn|group=note|name=Videoton}}

|attendance = 1,858

|referee = Mads-Kristoffer Kristoffersen (Denmark)

|report = https://www.uefa.com/uefaeuropaleague/match/2020097/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 20:30

|team1 = Čukarički {{fbaicon|SRB}}

|score = 1–1

|team2 = {{fbaicon|HUN}} Videoton

|goals1 =

• Fofana {{goal|13}}

|goals2 =

• Géresi {{goal|76}}

|stadium = Čukarički Stadium, Belgrade

|attendance = 1,653

|referee = Alexandre Boucaut (Belgium)

|report = https://www.uefa.com/uefaeuropaleague/match/2020137/

}}

Videoton won 3–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 20:45

|team1 = Cliftonville {{fbaicon|NIR}}

|score = 2–3

|team2 = {{fbaicon|CYP}} AEK Larnaca

|goals1 =

• McGuinness {{goal|18}}
• J. Donnelly {{goal|50}}

|goals2 =

• Tričkovski {{goal|59}}
• Charalambous {{goal|64}}
• Joan Tomàs {{goal|77}}

|stadium = Solitude, Belfast

|attendance = 1,352

|referee = Adrien Jaccottet (Switzerland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020098/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 19:00

|team1 = AEK Larnaca {{fbaicon|CYP}}

|score = 2–0

|team2 = {{fbaicon|NIR}} Cliftonville

|goals1 =

• Boljević {{goal|45}}
• Joan Tomàs {{goal|48}}

|goals2 =

|stadium = Antonis Papadopoulos Stadium, Larnaca{{refn|group=note|name=AEK Larnaca}}

|attendance = 2,112

|referee = Tihomir Pejin (Croatia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020138/

}}

AEK Larnaca won 5–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 19:00

|team1 = AIK {{fbaicon|SWE}}

|score = 1–0

|team2 = {{fbaicon|GIB}} Europa

|goals1 =

• Strandberg {{goal|89}}

|goals2 =

|stadium = Friends Arena, Solna

|attendance = 5,250

|referee = Ognjen Valjić (Bosnia and Herzegovina)

|report = https://www.uefa.com/uefaeuropaleague/match/2020099/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 19:00

|team1 = Europa {{fbaicon|GIB}}

|score = 0–1

|team2 = {{fbaicon|SWE}} AIK

|goals1 =

|goals2 =

• Markkanen {{goal|55}}

|stadium = Victoria Stadium, Gibraltar

|attendance = 1,145

|referee = Ádám Farkas (Hungary)

|report = https://www.uefa.com/uefaeuropaleague/match/2020139/

}}

AIK won 2–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 18:00

|team1 = Levadia Tallinn {{fbaicon|EST}}

|score = 3–1

|team2 = {{fbaicon|CZE}} Slavia Prague

|goals1 =

• Hunt {{goal|35}}
• Gando {{goal|67}}
• Antonov {{goal|90}}

|goals2 =

• Mingazow {{goal|63}}

|stadium = Kadriorg Stadium, Tallinn

|attendance = 2,750

|referee = Neil Doyle (Republic of Ireland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020100/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 19:00

|team1 = Slavia Prague {{fbaicon|CZE}}

|score = 2–0

|team2 = {{fbaicon|EST}} Levadia Tallinn

|goals1 =

• Škoda {{goal|10}}
• Van Kessel {{goal|67}}

|goals2 =

|stadium = Eden Arena, Prague

|attendance = 14,856

|referee = Christos Nicolaides (Cyprus)

|report = https://www.uefa.com/uefaeuropaleague/match/2020140/

}}

3–3 on aggregate; Slavia Prague won on away goals.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 20:00

|team1 = Genk {{fbaicon|BEL}}

|score = 2–0

|team2 = {{fbaicon|MNE}} Budućnost Podgorica

|goals1 =

• Kebano {{goal|17|pen.}}
• Samatta {{goal|79}}

|goals2 =

|stadium = Luminus Arena, Genk

|attendance = 10,450

|referee = Vilhjálmur Alvar Þórarinsson (Iceland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020101/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 20:45

|team1 = Budućnost Podgorica {{fbaicon|MNE}}

|score = 2–0

|aet = yes

|team2 = {{fbaicon|BEL}} Genk

|goals1 =

• Đalović {{goal|1}}
• Raičković {{goal|40}}

|goals2 =

|stadium = City Stadium, Podgorica

|attendance = 4,500

|referee = Charalambos Kalogeropoulos (Greece)

|penalties1 =

• Radunović {{pengoal}}
• Raspopović {{penmiss}}
• Đalović {{pengoal}}
• Mirković {{penmiss}}

|penaltyscore = 2–4

|penalties2 =

• {{pengoal}} Buffel
• {{pengoal}} Heynen
• {{pengoal}} Samatta
• {{pengoal}} Wouters

|report = https://www.uefa.com/uefaeuropaleague/match/2020141/

}}

2–2 on aggregate; Genk won 4–2 on penalties.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|14|df=y}}

|time = 19:00

|team1 = SønderjyskE {{fbaicon|DEN}}

|score = 2–1

|team2 = {{fbaicon|NOR}} Strømsgodset

|goals1 =

• Kløve {{goal|9}}
• Uhre {{goal|82}}

|goals2 =

• Pedersen {{goal|16}}

|stadium = Sydbank Park, Haderslev

|attendance = 4,795

|referee = Georgi Kabakov (Bulgaria)

|report = https://www.uefa.com/uefaeuropaleague/match/2020102/

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|21|df=y}}

|time = 19:00

|team1 = Strømsgodset {{fbaicon|NOR}}

|score = 2–2

|aet = yes

|team2 = {{fbaicon|DEN}} SønderjyskE

|goals1 =

• Keita {{goal|17||45+2}}

|goals2 =

• Uhre {{goal|69}}
• Kløve {{goal|120}}

|stadium = Marienlyst Stadion, Drammen

|attendance = 3,875

|referee = Steven McLean (Scotland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020142/

}}

SønderjyskE won 4–3 on aggregate.

A total of 58 teams played in the third qualifying round: 25 teams which entered in this round, and the 33 winners of the second qualifying round. The draw was held on 15 July 2016.{{cite web |title=Europa League third qualifying round draw |url=https://www.uefa.com/uefaeuropaleague/news/022f-0e94972686fa-dae3912cfc36-1000--europa-league-third-qualifying-round-draw/ |website=UEFA |publisher=Union of European Football Associations |date=15 July 2016 |access-date=15 July 2016}} Teams were pre-assigned numbers by UEFA so that the draw could be held in one run for the group with 10 teams and another run for all groups with 12 teams.

class="wikitable" style="font-size:85%"
colspan=2|Group 1 !colspan=2|Group 2 !colspan=2|Group 3
Seeded !Unseeded !Seeded !Unseeded !Seeded !Unseeded
valign=top| {{fbaicon|FRA}} Saint-Étienne {{small|(1)}} {{fbaicon|ISR}} Maccabi Tel Aviv{{Cref2|†|group=2}} {{small|(2)}} {{fbaicon|RUS}} Spartak Moscow {{small|(3)}} {{fbaicon|UKR}} Vorskla Poltava {{small|(4)}} {{fbaicon|BLR}} Dinamo Minsk{{Cref2|†|group=2}} {{small|(5)}} |valign=top| {{fbaicon|CYP}} AEK Larnaca{{Cref2|†|group=2}} {{small|(6)}} {{fbaicon|GRE}} AEK Athens {{small|(7)}} {{fbaicon|SRB}} Vojvodina{{Cref2|†|group=2}} {{small|(8)}} {{fbaicon|ROU}} Pandurii Târgu Jiu {{small|(9)}} {{fbaicon|CRO}} Lokomotiva Zagreb{{Cref2|†|group=2}} {{small|(10)}} |valign=top| {{fbaicon|NED}} AZ {{small|(1)}} {{fbaicon|RUS}} Krasnodar {{small|(2)}} {{fbaicon|POL}} Zagłębie Lubin{{Cref2|†|group=2}} {{small|(3)}} {{fbaicon|ITA}} Sassuolo {{small|(4)}} {{fbaicon|POR}} Rio Ave {{small|(5)}} {{fbaicon|ISR}} Beitar Jerusalem{{Cref2|†|group=2}} {{small|(6)}} |valign=top| {{fbaicon|LVA}} Jelgava{{Cref2|†|group=2}} {{small|(7)}} {{fbaicon|SUI}} Luzern {{small|(8)}} {{fbaicon|DEN}} SønderjyskE{{Cref2|†|group=2}} {{small|(9)}} {{fbaicon|CZE}} Slavia Prague{{Cref2|†|group=2}} {{small|(10)}} {{fbaicon|MLT}} Birkirkara{{Cref2|†|group=2}} {{small|(11)}} {{fbaicon|GRE}} PAS Giannina{{Cref2|†|group=2}} {{small|(12)}} |valign=top| {{fbaicon|FRA}} Lille {{small|(1)}} {{fbaicon|SVN}} Maribor{{Cref2|†|group=2}} {{small|(2)}} {{fbaicon|AUT}} Austria Wien{{Cref2|†|group=2}} {{small|(3)}} {{fbaicon|GRE}} Panathinaikos {{small|(4)}} {{fbaicon|EST}} Nõmme Kalju{{Cref2|†|group=2}} {{small|(5)}} {{fbaicon|CRO}} Hajduk Split{{Cref2|†|group=2}} {{small|(6)}} |valign=top| {{fbaicon|UKR}} Oleksandriya {{small|(7)}} {{fbaicon|SWE}} AIK{{Cref2|†|group=2}} {{small|(8)}} {{fbaicon|SVK}} Spartak Trnava{{Cref2|†|group=2}} {{small|(9)}} {{fbaicon|TUR}} Osmanlıspor{{Cref2|†|group=2}} {{small|(10)}} {{fbaicon|SCO}} Aberdeen{{Cref2|†|group=2}} {{small|(11)}} {{fbaicon|AZE}} Gabala{{Cref2|†|group=2}} {{small|(12)}}
colspan=2|Group 4 !colspan=2|Group 5 !rowspan=3 colspan=2|
Seeded !Unseeded !Seeded !Unseeded
valign=top| {{fbaicon|BEL}} Genk{{Cref2|†|group=2}} {{small|(1)}} {{fbaicon|AUT}} Rapid Wien {{small|(2)}} {{fbaicon|GER}} Hertha BSC {{small|(3)}} {{fbaicon|CRO}} Rijeka {{small|(4)}} {{fbaicon|POR}} Arouca {{small|(5)}} {{fbaicon|CZE}} Mladá Boleslav {{small|(6)}} |valign=top| {{fbaicon|MKD}} Shkëndija{{Cref2|†|group=2}} {{small|(7)}} {{fbaicon|TUR}} İstanbul Başakşehir {{small|(8)}} {{fbaicon|DEN}} Brøndby{{Cref2|†|group=2}} {{small|(9)}} {{fbaicon|NED}} Heracles Almelo {{small|(10)}} {{fbaicon|BLR}} Torpedo-BelAZ Zhodino{{Cref2|†|group=2}} {{small|(11)}} {{fbaicon|IRL}} Cork City{{Cref2|†|group=2}} {{small|(12)}} |valign=top| {{fbaicon|BEL}} Gent {{small|(1)}} {{fbaicon|CZE}} Slovan Liberec {{small|(2)}} {{fbaicon|ENG}} West Ham United {{small|(3)}} {{fbaicon|DEN}} Midtjylland{{Cref2|†|group=2}} {{small|(4)}} {{fbaicon|FIN}} HJK{{Cref2|†|group=2}} {{small|(5)}} {{fbaicon|CYP}} Apollon Limassol {{small|(6)}} |valign=top| {{fbaicon|SUI}} Grasshopper{{Cref2|†|group=2}} {{small|(7)}} {{fbaicon|HUN}} Videoton{{Cref2|†|group=2}} {{small|(8)}} {{fbaicon|SVN}} Domžale{{Cref2|†|group=2}} {{small|(9)}} {{fbaicon|SWE}} IFK Göteborg{{Cref2|†|group=2}} {{small|(10)}} {{fbaicon|AUT}} Admira Wacker Mödling{{Cref2|†|group=2}} {{small|(11)}} {{fbaicon|ROU}} Viitorul Constanța {{small|(12)}}

;Notes

{{Cnote2 Begin|liststyle=disc}}

{{Cnote2|†|n=0|group=2|^† Winners of the second qualifying round whose identity was not known at the time of the draw. Teams in italics defeated a team with a higher coefficient in the second qualifying round, thus effectively taking the coefficient of their defeated opponent in the draw for the third qualifying round.}}

{{Cnote2 End}}

The first legs were played on 28 July, and the second legs were played on 3 and 4 August 2016.

{{#invoke:Sports series|main|generate_links=y

|Lokomotiva Zagreb|CRO|3–2|Vorskla Poltava|UKR|0–0|3–2

|Saint-Étienne|FRA|1–0|AEK Athens|GRE|0–0|1–0

|AEK Larnaca|CYP|2–1|Spartak Moscow|RUS|1–1|1–0

|Pandurii Târgu Jiu|ROU|2–5|Maccabi Tel Aviv|ISR|1–3|1–2

|Vojvodina|SRB|3–1|Dinamo Minsk|BLR|1–1|2–0

|Zagłębie Lubin|POL|2–3|SønderjyskE|DEN|1–2|1–1

|Luzern|SUI|1–4|Sassuolo|ITA|1–1|0–3

|Slavia Prague|CZE|1–1 (a)|Rio Ave|POR|0–0|1–1

|Birkirkara|MLT|1–6|Krasnodar|RUS|0–3|1–3

|AZ|NED|3–1|PAS Giannina|GRE|1–0|2–1

|Jelgava|LVA|1–4|Beitar Jerusalem|ISR|1–1|0–3

|Austria Wien|AUT|1–1 (5–4 p)|Spartak Trnava|SVK|0–1|1–0 (aet)

|Panathinaikos|GRE|3–0|AIK|SWE|1–0|2–0

|Osmanlıspor|TUR|3–0|Nõmme Kalju|EST|1–0|2–0

|Aberdeen|SCO|1–2|Maribor|SVN|1–1|0–1

|Lille|FRA|1–2|Gabala|AZE|1–1|0–1

|Oleksandriya|UKR|1–6|Hajduk Split|CRO|0–3|1–3

|Hertha BSC|GER|2–3|Brøndby|DEN|1–0|1–3

|İstanbul Başakşehir|TUR|2–2 (a)|Rijeka|CRO|0–0|2–2

|Heracles Almelo|NED|1–1 (a)|Arouca|POR|1–1|0–0

|Torpedo-BelAZ Zhodino|BLR|0–3|Rapid Wien|AUT|0–0|0–3

|Genk|BEL|3–1|Cork City|IRL|1–0|2–1

|Shkëndija|MKD|2–1|Mladá Boleslav|CZE|2–0|0–1

|Domžale|SVN|2–4|West Ham United|ENG|2–1|0–3

|Videoton|HUN|1–2|Midtjylland|DEN|0–1|1–1 (aet)

|IFK Göteborg|SWE|3–2|HJK|FIN|1–2|2–0

|Admira Wacker Mödling|AUT|1–4|Slovan Liberec|CZE|1–2|0–2

|Gent|BEL|5–0|Viitorul Constanța|ROU|5–0|0–0

|Grasshopper|SUI|5–4|Apollon Limassol|CYP|2–1|3–3 (aet)

|note_agg_13=Order of legs reversed after original draw.

|note_agg_24=agg_13

}}

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 19:00

|team1 = Lokomotiva Zagreb {{fbaicon|CRO}}

|score = 0–0

|team2 = {{fbaicon|UKR}} Vorskla Poltava

|goals1 =

|goals2 =

|stadium = Stadion Maksimir, Zagreb{{refn|group=note|name=Lokomotiva|Lokomotiva played their third qualifying and play-off rounds home matches at Stadion Maksimir, Zagreb, instead of their regular stadium Stadion Kranjčevićeva, Zagreb.}}

|attendance = 328{{cite web |title=Summary UEFA Europa League - Round 3 |url=https://int.soccerway.com/international/europe/uefa-cup/20162017/3rd-qualifying-round/r35525/ |publisher=Soccerway |access-date=5 August 2016}}

|referee = Harald Lechner (Austria)

|report = https://www.uefa.com/uefaeuropaleague/match/2020367/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 19:00

|team1 = Vorskla Poltava {{fbaicon|UKR}}

|score = 2–3

|team2 = {{fbaicon|CRO}} Lokomotiva Zagreb

|goals1 =

• Perić {{goal|49|o.g.}}
• Chesnakov {{goal|74}}

|goals2 =

• Bočkaj {{goal|1}}
• Fiolić {{goal|53}}
• Perić {{goal|64}}

|stadium = Oleksiy Butovskyi Vorskla Stadium, Poltava

|attendance = 12,000

|referee = Orel Grinfeeld (Israel)

|report = https://www.uefa.com/uefaeuropaleague/match/2020396/

}}

Lokomotiva Zagreb won 3–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 21:00

|team1 = Saint-Étienne {{fbaicon|FRA}}

|score = 0–0

|team2 = {{fbaicon|GRE}} AEK Athens

|goals1 =

|goals2 =

|stadium = Stade Geoffroy-Guichard, Saint-Étienne

|attendance = 30,438

|referee = Antonio Damato (Italy)

|report = https://www.uefa.com/uefaeuropaleague/match/2020368/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 20:00

|team1 = AEK Athens {{fbaicon|GRE}}

|score = 0–1

|team2 = {{fbaicon|FRA}} Saint-Étienne

|goals1 =

|goals2 =

• Berić {{goal|23}}

|stadium = Olympic Stadium, Athens

|attendance = 25,004

|referee = Alon Yefet (Israel)

|report = https://www.uefa.com/uefaeuropaleague/match/2020397/

}}

Saint-Étienne won 1–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 17:00

|team1 = AEK Larnaca {{fbaicon|CYP}}

|score = 1–1

|team2 = {{fbaicon|RUS}} Spartak Moscow

|goals1 =

• Alves {{goal|65}}

|goals2 =

• Ananidze {{goal|38}}

|stadium = Antonis Papadopoulos Stadium, Larnaca{{refn|group=note|name=AEK Larnaca}}

|attendance = 4,323

|referee = Alejandro Hernández Hernández (Spain)

|report = https://www.uefa.com/uefaeuropaleague/match/2020369/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 18:30

|team1 = Spartak Moscow {{fbaicon|RUS}}

|score = 0–1

|team2 = {{fbaicon|CYP}} AEK Larnaca

|goals1 =

|goals2 =

• Tričkovski {{goal|89}}

|stadium = Otkrytiye Arena, Moscow

|attendance = 24,017

|referee = Alexander Harkam (Austria)

|report = https://www.uefa.com/uefaeuropaleague/match/2020398/

}}

AEK Larnaca won 2–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 20:00

|team1 = Pandurii Târgu Jiu {{fbaicon|ROU}}

|score = 1–3

|team2 = {{fbaicon|ISR}} Maccabi Tel Aviv

|goals1 =

• Herea {{goal|30}}

|goals2 =

• Ben Haim II {{goal|7}}
• Igiebor {{goal|49}}
• Micha {{goal|77}}

|stadium = Stadionul Municipal, Drobeta-Turnu Severin{{refn|group=note|name=Pandurii Târgu Jiu|Pandurii Târgu Jiu played their home match at Stadionul Municipal, Drobeta-Turnu Severin, instead of their regular stadium Stadionul Tudor Vladimirescu, Târgu Jiu, due to renovations.{{cite web |title=Pandurii vrea să joace meciurile din Europa la Severin. Reprezentanții UEFA au inspectat arena |trans-title=Pandurii want to play European matches at Severin. UEFA representatives have inspected the arena |language=ro |url=http://www.digisport.ro/Sport/FOTBAL/Competitii/Liga+1/Pandurii+vrea+sa+joace+meciurile+din+Europa+la+Severin+Reprezent |website=digisport.ro |publisher=DigiSport |date=25 June 2016 |access-date=15 July 2016}}{{cite web |title=Pandurii a primit acceptul UEFA. Poate juca la Drobeta Turnu Severin în turul 3 al Europa League |trans-title=Pandurii received UEFA approval. They can play in Drobeta-Turnu Severin for the Europa League third qualifying round |language=ro |url=http://www.digisport.ro/Sport/FOTBAL/Competitii/Europa+League/Pandurii+a+primit+acceptul+UEFA+Poate+juca+la+Drobeta+Turnu+Seve |website=digisport.ro |publisher=DigiSport |date=15 July 2016 |access-date=15 July 2016}}}}

|attendance = 4,058

|referee = Serhiy Boyko (Ukraine)

|report = https://www.uefa.com/uefaeuropaleague/match/2020370/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 19:30

|team1 = Maccabi Tel Aviv {{fbaicon|ISR}}

|score = 2–1

|team2 = {{fbaicon|ROU}} Pandurii Târgu Jiu

|goals1 =

• Igiebor {{goal|24}}
• Scarione {{goal|80}}

|goals2 =

• Pleașcă {{goal|57}}

|stadium = Netanya Stadium, Netanya{{refn|group=note|name=Maccabi Tel Aviv}}

|attendance = 8,126

|referee = Serge Gumienny (Belgium)

|report = https://www.uefa.com/uefaeuropaleague/match/2020399/

}}

Maccabi Tel Aviv won 5–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 20:00

|team1 = Vojvodina {{fbaicon|SRB}}

|score = 1–1

|team2 = {{fbaicon|BLR}} Dinamo Minsk

|goals1 =

• Babić {{goal|29}}

|goals2 =

• Budnik {{goal|83}}

|stadium = Karađorđe Stadium, Novi Sad

|attendance = 8,346

|referee = Oliver Drachta (Austria)

|report = https://www.uefa.com/uefaeuropaleague/match/2020371/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 19:45

|team1 = Dinamo Minsk {{fbaicon|BLR}}

|score = 0–2

|team2 = {{fbaicon|SRB}} Vojvodina

|goals1 =

|goals2 =

• Babić {{goal|32}}
• Antić {{goal|81}}

|stadium = Regional Sport Complex Brestsky, Brest{{refn|group=note|name=Dinamo Minsk|Dinamo Minsk played their third qualifying round home match at Regional Sport Complex Brestsky, Brest, instead of their regular stadium Traktor Stadium, Minsk.}}

|attendance = 7,500

|referee = Sébastien Delferière (Belgium)

|report = https://www.uefa.com/uefaeuropaleague/match/2020400/

}}

Vojvodina won 3–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 19:00

|team1 = Zagłębie Lubin {{fbaicon|POL}}

|score = 1–2

|team2 = {{fbaicon|DEN}} SønderjyskE

|goals1 =

• Janoszka {{goal|45+2}}

|goals2 =

• Kroon {{goal|19}}
• Dal Hende {{goal|36}}

|stadium = Stadion Zagłębia Lubin, Lubin

|attendance = 10,271

|referee = Bobby Madley (England)

|report = https://www.uefa.com/uefaeuropaleague/match/2020372/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 19:15

|team1 = SønderjyskE {{fbaicon|DEN}}

|score = 1–1

|team2 = {{fbaicon|POL}} Zagłębie Lubin

|goals1 =

• Pedersen {{goal|65}}

|goals2 =

• Guldan {{goal|22}}

|stadium = Sydbank Park, Haderslev

|attendance = 4,795

|referee = Tamás Bognár (Hungary)

|report = https://www.uefa.com/uefaeuropaleague/match/2020401/

}}

SønderjyskE won 3–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 19:45

|team1 = Luzern {{fbaicon|SUI}}

|score = 1–1

|team2 = {{fbaicon|ITA}} Sassuolo

|goals1 =

• M. Schneuwly {{goal|8}}

|goals2 =

• Berardi {{goal|42|pen.}}

|stadium = Swissporarena, Lucerne

|attendance = 10,555

|referee = Andreas Ekberg (Sweden)

|report = https://www.uefa.com/uefaeuropaleague/match/2020373/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 20:30

|team1 = Sassuolo {{fbaicon|ITA}}

|score = 3–0

|team2 = {{fbaicon|SUI}} Luzern

|goals1 =

• Berardi {{goal|19||39|pen.}}
• Defrel {{goal|64}}

|goals2 =

|stadium = Mapei Stadium – Città del Tricolore, Reggio Emilia

|attendance = 13,415

|referee = Ali Palabıyık (Turkey)

|report = https://www.uefa.com/uefaeuropaleague/match/2020402/

}}

Sassuolo won 4–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 19:00

|team1 = Slavia Prague {{fbaicon|CZE}}

|score = 0–0

|team2 = {{fbaicon|POR}} Rio Ave

|goals1 =

|goals2 =

|stadium = Eden Arena, Prague

|attendance = 15,082

|referee = Sergey Lapochkin (Russia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020374/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 21:00

|team1 = Rio Ave {{fbaicon|POR}}

|score = 1–1

|team2 = {{fbaicon|CZE}} Slavia Prague

|goals1 =

• Ribeiro {{goal|57}}

|goals2 =

• Hušbauer {{goal|22}}

|stadium = Estádio dos Arcos, Vila do Conde

|attendance = 6,081

|referee = Andrew Dallas (Scotland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020403/

}}

1–1 on aggregate; Slavia Prague won on away goals.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 19:30

|team1 = Birkirkara {{fbaicon|MLT}}

|score = 0–3

|team2 = {{fbaicon|RUS}} Krasnodar

|goals1 =

|goals2 =

• Granqvist {{goal|45+1}}
• Smolov {{goal|75|pen.}}
• Laborde {{goal|89}}

|stadium = Hibernians Stadium, Paola{{refn|group=note|name=Birkirkara}}

|attendance = 1,560

|referee = Bart Vertenten (Belgium)

|report = https://www.uefa.com/uefaeuropaleague/match/2020375/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 18:30

|team1 = Krasnodar {{fbaicon|RUS}}

|score = 3–1

|team2 = {{fbaicon|MLT}} Birkirkara

|goals1 =

• Eboue {{goal|15}}
• Joãozinho {{goal|37}}
• Laborde {{goal|38}}

|goals2 =

• Jović {{goal|61}}

|stadium = Kuban Stadium, Krasnodar

|attendance = 7,256

|referee = Aliyar Aghayev (Azerbaijan)

|report = https://www.uefa.com/uefaeuropaleague/match/2020404/

}}

Krasnodar won 6–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 20:45

|team1 = AZ {{fbaicon|NED}}

|score = 1–0

|team2 = {{fbaicon|GRE}} PAS Giannina

|goals1 =

• Luckassen {{goal|36}}

|goals2 =

|stadium = AFAS Stadion, Alkmaar

|attendance = 9,156

|referee = Mattias Gestranius (Finland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020376/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 20:00

|team1 = PAS Giannina {{fbaicon|GRE}}

|score = 1–2

|team2 = {{fbaicon|NED}} AZ

|goals1 =

• Conde {{goal|9}}

|goals2 =

• Dabney {{goal|29}}
• Luckassen {{goal|36}}

|stadium = Peristeri Stadium, Peristeri{{refn|group=note|name=PAS Giannina|PAS Giannina played their third qualifying round home match at Peristeri Stadium, Peristeri, instead of their regular stadium Zosimades Stadium, Ioannina.}}

|attendance = 3,373

|referee = Robert Schörgenhofer (Austria)

|report = https://www.uefa.com/uefaeuropaleague/match/2020405/

}}

AZ won 3–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 19:00

|team1 = Jelgava {{fbaicon|LVA}}

|score = 1–1

|team2 = {{fbaicon|ISR}} Beitar Jerusalem

|goals1 =

• Smirnovs {{goal|70}}

|goals2 =

• Vered {{goal|25}}

|stadium = Skonto Stadium, Riga{{refn|group=note|name=Jelgava|Jelgava played their third qualifying round home match at Skonto Stadium, Riga, instead of their regular stadium Olympic Sports Center of Zemgale, Jelgava.}}

|attendance = 2,886

|referee = Georgi Kabakov (Bulgaria)

|report = https://www.uefa.com/uefaeuropaleague/match/2020377/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 19:00

|team1 = Beitar Jerusalem {{fbaicon|ISR}}

|score = 3–0

|team2 = {{fbaicon|LVA}} Jelgava

|goals1 =

• Atzili {{goal|16|pen.}}
• Shechter {{goal|29}}
• Heister {{goal|47}}

|goals2 =

|stadium = Teddy Stadium, Jerusalem

|attendance = 16,175

|referee = Hugo Miguel (Portugal)

|report = https://www.uefa.com/uefaeuropaleague/match/2020406/

}}

Beitar Jerusalem won 4–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 19:00

|team1 = Austria Wien {{fbaicon|AUT}}

|score = 0–1

|team2 = {{fbaicon|SVK}} Spartak Trnava

|goals1 =

|goals2 =

• Tambe {{goal|46}}

|stadium = Ernst-Happel-Stadion, Vienna{{refn|group=note|name=Austria Wien}}

|attendance = 6,835

|referee = Alexandru Tudor (Romania)

|report = https://www.uefa.com/uefaeuropaleague/match/2020378/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 18:30

|team1 = Spartak Trnava {{fbaicon|SVK}}

|score = 0–1

|aet = yes

|team2 = {{fbaicon|AUT}} Austria Wien

|goals1 =

|goals2 =

• Friesenbichler {{goal|88}}

|stadium = Štadión Antona Malatinského, Trnava

|attendance = 17,152

|referee = Ivan Bebek (Croatia)

|penalties1 =

• Godál {{pengoal}}
• Schranz {{pengoal}}
• Sloboda {{pengoal}}
• Jirka {{pengoal}}
• Mikovič {{penmiss}}

|penaltyscore = 4–5

|penalties2 =

• {{pengoal}} Larsen
• {{pengoal}} Tajouri
• {{pengoal}} Kvasina
• {{pengoal}} Serbest
• {{pengoal}} Friesenbichler

|report = https://www.uefa.com/uefaeuropaleague/match/2020407/

}}

1–1 on aggregate; Austria Wien won 5–4 on penalties.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 20:00

|team1 = Panathinaikos {{fbaicon|GRE}}

|score = 1–0

|team2 = {{fbaicon|SWE}} AIK

|goals1 =

• Moledo {{goal|79}}

|goals2 =

|stadium = Leoforos Alexandras Stadium, Athens

|attendance = 12,021

|referee = Bastian Dankert (Germany)

|report = https://www.uefa.com/uefaeuropaleague/match/2020379/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 19:00

|team1 = AIK {{fbaicon|SWE}}

|score = 0–2

|team2 = {{fbaicon|GRE}} Panathinaikos

|goals1 =

|goals2 =

• Ibarbo {{goal|46}}
• Berg {{goal|73}}

|stadium = Tele2 Arena, Stockholm{{refn|group=note|name=AIK}}

|attendance = 15,175

|referee = Tony Chapron (France)

|report = https://www.uefa.com/uefaeuropaleague/match/2020408/

}}

Panathinaikos won 3–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 20:00

|team1 = Osmanlıspor {{fbaicon|TUR}}

|score = 1–0

|team2 = {{fbaicon|EST}} Nõmme Kalju

|goals1 =

• Pinto {{goal|74}}

|goals2 =

|stadium = Osmanlı Stadyumu, Ankara

|attendance = 8,634

|referee = Nikola Dabanović (Montenegro)

|report = https://www.uefa.com/uefaeuropaleague/match/2020380/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 18:00

|team1 = Nõmme Kalju {{fbaicon|EST}}

|score = 0–2

|team2 = {{fbaicon|TUR}} Osmanlıspor

|goals1 =

|goals2 =

• Çürüksu {{goal|4}}
• Delarge {{goal|29}}

|stadium = Kadriorg Stadium, Tallinn{{refn|group=note|name=Nõmme Kalju}}

|attendance = 2,235

|referee = Christian Dingert (Germany)

|report = https://www.uefa.com/uefaeuropaleague/match/2020409/

}}

Osmanlıspor won 3–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 20:45

|team1 = Aberdeen {{fbaicon|SCO}}

|score = 1–1

|team2 = {{fbaicon|SVN}} Maribor

|goals1 =

• Hayes {{goal|88}}

|goals2 =

• Novaković {{goal|83}}

|stadium = Pittodrie Stadium, Aberdeen

|attendance = 17,105

|referee = Tore Hansen (Norway)

|report = https://www.uefa.com/uefaeuropaleague/match/2020381/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 20:15

|team1 = Maribor {{fbaicon|SVN}}

|score = 1–0

|team2 = {{fbaicon|SCO}} Aberdeen

|goals1 =

• Shinnie {{goal|90+3|o.g.}}

|goals2 =

|stadium = Ljudski vrt, Maribor

|attendance = 9,796

|referee = Nikola Popov (Bulgaria)

|report = https://www.uefa.com/uefaeuropaleague/match/2020410/

}}

Maribor won 2–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 19:00

|team1 = Lille {{fbaicon|FRA}}

|score = 1–1

|team2 = {{fbaicon|AZE}} Gabala

|goals1 =

• Mendes {{goal|47}}

|goals2 =

• Vernydub {{goal|13}}

|stadium = Stadium Lille Métropole, Villeneuve-d'Ascq{{refn|group=note|name=Lille|Lille played their home match at Stadium Lille Métropole, Villeneuve-d'Ascq, instead of their regular stadium Stade Pierre-Mauroy, Villeneuve-d'Ascq.{{cite web |title=LOSC: Obligé de changer (encore) de pelouse, Lille jouera son premier match européen...au Stadium ! |trans-title=LOSC: Forced to change lawn (again), Lille will play their first European game... at the Stadium! |language=fr |url=http://www.20minutes.fr/lille/1889471-20160713-losc-oblige-changer-encore-pelouse-lille-jouera-premier-match-europeen-stadium |website=20minutes.fr |publisher=20 Minutes |date=13 July 2016 |access-date=19 July 2016}}}}

|attendance = 8,265

|referee = Daniel Stefański (Poland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020382/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 19:00

|team1 = Gabala {{fbaicon|AZE}}

|score = 1–0

|team2 = {{fbaicon|FRA}} Lille

|goals1 =

• Ozobić {{goal|34}}

|goals2 =

|stadium = Bakcell Arena, Baku{{refn|group=note|name=Gabala}}

|attendance = 10,550

|referee = Aleksei Eskov (Russia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020411/

}}

Gabala won 2–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 18:30

|team1 = Oleksandriya {{fbaicon|UKR}}

|score = 0–3

|team2 = {{fbaicon|CRO}} Hajduk Split

|goals1 =

|goals2 =

• Ćosić {{goal|53}}
• Erceg {{goal|82}}
• Ohandza {{goal|90}}

|stadium = CSC Nika Stadium, Oleksandriia

|attendance = 6,800

|referee = Gediminas Mažeika (Lithuania)

|report = https://www.uefa.com/uefaeuropaleague/match/2020383/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 20:30

|team1 = Hajduk Split {{fbaicon|CRO}}

|score = 3–1

|team2 = {{fbaicon|UKR}} Oleksandriya

|goals1 =

• Nižić {{goal|21}}
• Sušić {{goal|52|pen.|56}}

|goals2 =

• Starenkyi {{goal|13}}

|stadium = Stadion Poljud, Split

|attendance = 25,000

|referee = John Beaton (Scotland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020412/

}}

Hajduk Split won 6–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 20:15

|team1 = Hertha BSC {{fbaicon|GER}}

|score = 1–0

|team2 = {{fbaicon|DEN}} Brøndby

|goals1 =

• Ibišević {{goal|28}}

|goals2 =

|stadium = Friedrich-Ludwig-Jahn-Sportpark, Berlin{{refn|group=note|name=Hertha BSC|Hertha BSC played their home match at Friedrich-Ludwig-Jahn-Sportpark, Berlin, instead of their regular stadium Olympiastadion, Berlin.{{cite web |title=Europa-League-Qualifikation: Hertha BSC trifft auf Brøndby oder Hibernian |trans-title=Europa League qualification: Hertha BSC face Brøndby or Hibernian |language=de |url=http://www.spiegel.de/sport/fussball/europa-league-qualifikation-hertha-bsc-trifft-auf-broendby-oder-hibernian-a-1103215.html |website=spiegel.de |publisher=Spiegel Online |date=15 July 2016 |access-date=17 July 2016}}}}

|attendance = 18,454

|referee = Kevin Blom (Netherlands)

|report = https://www.uefa.com/uefaeuropaleague/match/2020384/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 20:15

|team1 = Brøndby {{fbaicon|DEN}}

|score = 3–1

|team2 = {{fbaicon|GER}} Hertha BSC

|goals1 =

• Pukki {{goal|3||34||52}}

|goals2 =

• Ibišević {{goal|30}}

|stadium = Brøndby Stadium, Brøndbyvester

|attendance = 17,102

|referee = Paweł Gil (Poland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020413/

}}

Brøndby won 3–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 19:30

|team1 = İstanbul Başakşehir {{fbaicon|TUR}}

|score = 0–0

|team2 = {{fbaicon|CRO}} Rijeka

|goals1 =

|goals2 =

|stadium = Başakşehir Fatih Terim Stadium, Istanbul

|attendance = 5,768

|referee = Svein-Erik Edvartsen (Norway)

|report = https://www.uefa.com/uefaeuropaleague/match/2020385/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 20:15

|team1 = Rijeka {{fbaicon|CRO}}

|score = 2–2

|team2 = {{fbaicon|TUR}} İstanbul Başakşehir

|goals1 =

• Bezjak {{goal|24||50|pen.}}

|goals2 =

• Višća {{goal|42||74}}

|stadium = Stadion Rujevica, Rijeka{{refn|group=note|name=Rijeka|Rijeka played their home match at Stadion Rujevica, Rijeka, instead of their regular stadium Stadion Kantrida, Rijeka, due to reconstruction.{{cite web |title=VIDEO: Nova Kantrida |trans-title=VIDEO: New Kantrida |language=hr |url=http://radio.hrt.hr/radio-rijeka/clanak/video-nova-kantrida/63426/ |website=radio.hrt.hr |publisher=Radio Rijeka |date=11 July 2014 |access-date=15 July 2016 |archive-date=5 March 2016 |archive-url=https://web.archive.org/web/20160305043339/http://radio.hrt.hr/radio-rijeka/clanak/video-nova-kantrida/63426/ |url-status=dead }}}}

|attendance = 5,524

|referee = Marius Avram (Romania)

|report = https://www.uefa.com/uefaeuropaleague/match/2020414/

}}

2–2 on aggregate; İstanbul Başakşehir won on away goals.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 18:45

|team1 = Heracles Almelo {{fbaicon|NED}}

|score = 1–1

|team2 = {{fbaicon|POR}} Arouca

|goals1 =

• Gladon {{goal|53}}

|goals2 =

• González {{goal|90+1}}

|stadium = Polman Stadion, Almelo

|attendance = 11,670

|referee = Charalambos Kalogeropoulos (Greece)

|report = https://www.uefa.com/uefaeuropaleague/match/2020386/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 19:00

|team1 = Arouca {{fbaicon|POR}}

|score = 0–0

|team2 = {{fbaicon|NED}} Heracles Almelo

|goals1 =

|goals2 =

|stadium = Estádio Municipal, Arouca

|attendance = 2,750

|referee = Adrien Jaccottet (Switzerland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020415/

}}

1–1 on aggregate; Arouca won on away goals.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 19:00

|team1 = Torpedo-BelAZ Zhodino {{fbaicon|BLR}}

|score = 0–0

|team2 = {{fbaicon|AUT}} Rapid Wien

|goals1 =

|goals2 =

|stadium = Torpedo Stadium, Zhodzina

|attendance = 3,940

|referee = Þorvaldur Árnason (Iceland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020387/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 21:05

|team1 = Rapid Wien {{fbaicon|AUT}}

|score = 3–0

|team2 = {{fbaicon|BLR}} Torpedo-BelAZ Zhodino

|goals1 =

• Pavelić {{goal|26}}
• Schrammel {{goal|36}}
• Schaub {{goal|90+2}}

|goals2 =

|stadium = Allianz Stadion, Vienna

|attendance = 18,600

|referee = Roi Reinshreiber (Israel)

|report = https://www.uefa.com/uefaeuropaleague/match/2020416/

}}

Rapid Wien won 3–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 20:00

|team1 = Genk {{fbaicon|BEL}}

|score = 1–0

|team2 = {{fbaicon|IRL}} Cork City

|goals1 =

• Bailey {{goal|31}}

|goals2 =

|stadium = Luminus Arena, Genk

|attendance = 7,765

|referee = Clayton Pisani (Malta)

|report = https://www.uefa.com/uefaeuropaleague/match/2020388/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 20:45

|team1 = Cork City {{fbaicon|IRL}}

|score = 1–2

|team2 = {{fbaicon|BEL}} Genk

|goals1 =

• Bennett {{goal|63}}

|goals2 =

• Buffel {{goal|13}}
• Dewaest {{goal|41}}

|stadium = Turners Cross, Cork

|attendance = 6,745

|referee = Kristo Tohver (Estonia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020417/

}}

Genk won 3–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 20:00

|team1 = Shkëndija {{fbaicon|MKD}}

|score = 2–0

|team2 = {{fbaicon|CZE}} Mladá Boleslav

|goals1 =

• Stênio Júnior {{goal|69}}
• Hasani {{goal|75}}

|goals2 =

|stadium = Philip II Arena, Skopje{{refn|group=note|name=Shkëndija}}

|attendance = 11,717

|referee = Artyom Kuchin (Kazakhstan)

|report = https://www.uefa.com/uefaeuropaleague/match/2020389/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 19:00

|team1 = Mladá Boleslav {{fbaicon|CZE}}

|score = 1–0

|team2 = {{fbaicon|MKD}} Shkëndija

|goals1 =

• Magera {{goal|82}}

|goals2 =

|stadium = Municipal Stadium, Mladá Boleslav

|attendance = 3,528

|referee = Simon Lee Evans (Wales)

|report = https://www.uefa.com/uefaeuropaleague/match/2020418/

}}

Shkëndija won 2–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 20:45

|team1 = Domžale {{fbaicon|SVN}}

|score = 2–1

|team2 = {{fbaicon|ENG}} West Ham United

|goals1 =

• Črnic {{goal|11|pen.|49}}

|goals2 =

• Noble {{goal|18|pen.}}

|stadium = Stožice Stadium, Ljubljana{{refn|group=note|name=Domžale|Domžale played their third qualifying round home match at Stožice Stadium, Ljubljana, instead of their regular stadium Sports Park, Domžale.}}

|attendance = 8,458

|referee = Mete Kalkavan (Turkey)

|report = https://www.uefa.com/uefaeuropaleague/match/2020390/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 20:45

|team1 = West Ham United {{fbaicon|ENG}}

|score = 3–0

|team2 = {{fbaicon|SVN}} Domžale

|goals1 =

• Kouyaté {{goal|8||25}}
• Feghouli {{goal|81}}

|goals2 =

|stadium = Olympic Stadium, London

|attendance = 53,914

|referee = Fredy Fautrel (France)

|report = https://www.uefa.com/uefaeuropaleague/match/2020419/

}}

West Ham United won 4–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 20:30

|team1 = Videoton {{fbaicon|HUN}}

|score = 0–1

|team2 = {{fbaicon|DEN}} Midtjylland

|goals1 =

|goals2 =

• Novák {{goal|55}}

|stadium = Pancho Arena, Felcsút{{refn|group=note|name=Videoton}}

|attendance = 2,899

|referee = Ville Nevalainen (Finland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020391/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 18:00

|team1 = Midtjylland {{fbaicon|DEN}}

|score = 1–1

|aet = yes

|team2 = {{fbaicon|HUN}} Videoton

|goals1 =

• Novák {{goal|104}}

|goals2 =

• Kovács {{goal|75}}

|stadium = MCH Arena, Herning

|attendance = 6,258

|referee = Marco Guida (Italy)

|report = https://www.uefa.com/uefaeuropaleague/match/2020420/

}}

Midtjylland won 2–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 19:00

|team1 = IFK Göteborg {{fbaicon|SWE}}

|score = 1–2

|team2 = {{fbaicon|FIN}} HJK

|goals1 =

• Salomonsson {{goal|73}}

|goals2 =

• Tanaka {{goal|47}}
• Morelos {{goal|75}}

|stadium = Gamla Ullevi, Gothenburg

|attendance = 9,046

|referee = Kevin Clancy (Scotland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020392/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 18:00

|team1 = HJK {{fbaicon|FIN}}

|score = 0–2

|team2 = {{fbaicon|SWE}} IFK Göteborg

|goals1 =

|goals2 =

• Boman {{goal|35}}
• Ankersen {{goal|82}}

|stadium = Sonera Stadium, Helsinki

|attendance = 10,107

|referee = Anatoliy Zhabchenko (Ukraine)

|report = https://www.uefa.com/uefaeuropaleague/match/2020421/

}}

IFK Göteborg won 3–2 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 21:05

|team1 = Admira Wacker Mödling {{fbaicon|AUT}}

|score = 1–2

|team2 = {{fbaicon|CZE}} Slovan Liberec

|goals1 =

• Knasmüllner {{goal|7}}

|goals2 =

• Vůch {{goal|11||69}}

|stadium = Bundesstadion Südstadt, Maria Enzersdorf

|attendance = 2,245

|referee = Halis Özkahya (Turkey)

|report = https://www.uefa.com/uefaeuropaleague/match/2020393/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|3|df=y}}

|time = 18:00

|team1 = Slovan Liberec {{fbaicon|CZE}}

|score = 2–0

|team2 = {{fbaicon|AUT}} Admira Wacker Mödling

|goals1 =

• Coufal {{goal|20}}
• Komlichenko {{goal|34|pen.}}

|goals2 =

|stadium = Stadion u Nisy, Liberec

|attendance = 6,125

|referee = Radu Petrescu (Romania)

|report = https://www.uefa.com/uefaeuropaleague/match/2020422/

}}

Slovan Liberec won 4–1 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 20:30

|team1 = Gent {{fbaicon|BEL}}

|score = 5–0

|team2 = {{fbaicon|ROU}} Viitorul Constanța

|goals1 =

• Mitrović {{goal|16}}
• Coulibaly {{goal|37||50}}
• Depoitre {{goal|56}}
• Neto {{goal|66}}

|goals2 =

|stadium = Ghelamco Arena, Ghent

|attendance = 12,332

|referee = Stephan Klossner (Switzerland)

|report = https://www.uefa.com/uefaeuropaleague/match/2020394/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 20:15

|team1 = Viitorul Constanța {{fbaicon|ROU}}

|score = 0–0

|team2 = {{fbaicon|BEL}} Gent

|goals1 =

|goals2 =

|stadium = Stadionul Viitorul, Ovidiu

|attendance = 1,294

|referee = Carlos del Cerro Grande (Spain)

|report = https://www.uefa.com/uefaeuropaleague/match/2020423/

}}

Gent won 5–0 on aggregate.

----

{{#invoke:football box|main

|date = {{Start date|2016|7|28|df=y}}

|time = 19:45

|team1 = Grasshopper {{fbaicon|SUI}}

|score = 2–1

|team2 = {{fbaicon|CYP}} Apollon Limassol

|goals1 =

• Tabaković {{goal|11}}
• Lavanchy {{goal|90+3}}

|goals2 =

• Guié Guié {{goal|76}}

|stadium = Kybunpark, St. Gallen{{refn|group=note|name=Grasshopper|Grasshopper played their third qualifying round home match at Kybunpark, St. Gallen, instead of their regular stadium Letzigrund, Zürich, which is booked for a Bruce Springsteen concert.{{cite web |title=Grasshoppers weiter, Vaduz gescheitert |trans-title=Grasshoppers get through, Vaduz failed to |language=de |url=http://www.luzernerzeitung.ch/sport/fussball/europacup/Grasshoppers-weiter-Vaduz-gescheitert;art2075,785081 |website=Luzerner Zeitung |publisher=Neue Luzerner Zeitung |date=21 July 2016 |access-date=22 July 2016 |archive-url=https://web.archive.org/web/20160728131355/http://www.luzernerzeitung.ch/sport/fussball/europacup/Grasshoppers-weiter-Vaduz-gescheitert;art2075,785081 |archive-date=28 July 2016 |url-status=dead |df=dmy-all }}}}

|attendance = 2,330

|referee = Andris Treimanis (Latvia)

|report = https://www.uefa.com/uefaeuropaleague/match/2020395/

}}

{{#invoke:football box|main

|date = {{Start date|2016|8|4|df=y}}

|time = 19:00

|team1 = Apollon Limassol {{fbaicon|CYP}}

|score = 3–3

|aet = yes

|team2 = {{fbaicon|SUI}} Grasshopper

|goals1 =

• Paulo Vinícius {{goal|73}}
• Papoulis {{goal|87}}
• Guié Guié {{goal|101}}

|goals2 =

• Andersen {{goal|77}}
• Caio {{goal|103}}
• Gjorgjev {{goal|120+1}}

|stadium = GSP Stadium, Nicosia{{refn|group=note|name=Apollon Limassol|Apollon Limassol played their home match at GSP Stadium, Nicosia, instead of their regular stadium Tsirion Stadium, Limassol.}}

|attendance = 5,887

|referee = Andre Marriner (England)

|report = https://www.uefa.com/uefaeuropaleague/match/2020424/

}}

Grasshopper won 5–4 on aggregate.