:Mainichi Film Award for Best Animation Film

! 1989

| Kiki's Delivery Service

| Studio Ghibli

| Hayao Miyazaki

! 1990

| Hashire! Shiroi Ōkami

| Group TAC

| Tsuneo Maeda

! 1991

| Roujin Z

| Tokyo Theaters Co.

| Hiroyuki Kitakubo

! 1992

| Porco Rosso

| Studio Ghibli

| Hayao Miyazaki

! 1993

| Patlabor 2: The Movie

| Production I.G

| Mamoru Oshii

! 1994

| Pom Poko

| Studio Ghibli

| Isao Takahata

! 1995

| Junkers Come Here

| Triangle Staff

| Junichi Sato

! 1996

| Black Jack

| Tezuka Productions

| Satoshi Kuwabara

! 1997

| Princess Mononoke

| Studio Ghibli

| Hayao Miyazaki

! 1998

| Doraemon: Nobita's Great Adventure in the South Seas

| Shin-Ei Animation

| Tsutomu Shibayama

! 1999

| Jin-Roh: The Wolf Brigade

| Production I.G

| Hiroyuki Okiura

! 2000

| Doraemon: A Grandmother's Recollections

| Shin-Ei Animation

| Ayumu Watanabe

! 2001

| Spirited Away

| Studio Ghibli

| Hayao Miyazaki

! 2002

| Crayon Shin-chan: The Storm Called: The Battle of the Warring States

| Shin-Ei Animation

| Keiichi Hara

! 2003

| Tokyo Godfathers

| Madhouse

| Satoshi Kon

! 2004

| The Place Promised in Our Early Days

| CoMix Wave Films

| Makoto Shinkai

! 2005

| Fullmetal Alchemist the Movie: Conqueror of Shamballa

| Bones

| Seiji Mizushima

! 2006

| The Girl Who Leapt Through Time

| Madhouse

| Mamoru Hosoda

! 2007

| Summer Days with Coo

| Shin-Ei Animation

| Keiichi Hara

! 2008

| The Sky Crawlers

| Production I.G

| Mamoru Oshii

! 2009

| Summer Wars

| Madhouse

| Mamoru Hosoda

! 2010

| Colorful

| Ascension

| Keiichi Hara

! 2011

| Hotarubi no Mori e

| Brain's Base

| Takahiro Omori

! 2012

| Wolf Children{{cite web |url= http://www.animenewsnetwork.com/news/2013-02-07/wolf-children-combustible-win-at-67th-mainichi-film-awards|title= Wolf Children, 'Combustible' Win at 67th Mainichi Film Awards|date=2013-02-07|access-date= 2013-02-08|work= Anime News Network}}

| Studio Chizu, Madhouse

| Mamoru Hosoda

! 2013

| The Tale of the Princess Kaguya{{cite web|url= http://www.filmbiz.asia/news/great-passage-pecoross-top-mainichi-award|title= Great Passage, Pecoross top Mainichi Award|author= Kevin Ma|date=21 January 2014|access-date= January 21, 2014|work= Film Business Asia|url-status= dead|archive-url= https://web.archive.org/web/20140803025017/http://www.filmbiz.asia/news/great-passage-pecoross-top-mainichi-award|archive-date=3 August 2014}}

| Studio Ghibli

| Isao Takahata

! 2014

| Giovanni's Island

| Production I.G

| Mizuho Nishikubo

! 2015

| Miss Hokusai

| Production I.G

| Keiichi Hara

! 2016

| Your Name

| CoMix Wave Films

| Makoto Shinkai

! 2017

| Complex × Complex

| Panpokopina

| Miyuki Fukuda

! 2018

| Okko's Inn

| DLE, Madhouse

| Kitaro Kosaka{{Cite web|url=https://mainichi.jp/mfa/history/|title=毎日映画コンクール 歴史（過去の受賞作）|website=Mainichi.jp|access-date=7 November 2021}}{{Cite web |url=https://www.gaga.co.jp/intls/detail/724 |title=ギャガ株式会社（GAGA Corporation）／Intls |access-date=2019-08-01 |archive-date=2019-08-01 |archive-url=https://web.archive.org/web/20190801003352/https://www.gaga.co.jp/intls/detail/724/ |url-status=dead }}

! 2019

| Children of the Sea

| Studio 4°C

| Ayumu Watanabe

! 2020

| Looking for Magical Doremi

| Toei Animation

| Haruka Kamatani, Junichi Sato

! 2021

| The House of the Lost on the Cape

| Aniplex

| Shin'ya Kawatsura

! 2022

| Takano Intersection

| (Independent production)

| Mizuki Ito

! 2023

| Maboroshi

| MAPPA

| Mari Okada