| Rank | Title | Revenue (¥) | Studios | Distributor | Release Dates |
| 1 | Kimetsu no Yaiba Movie: Mugen Ressha-hen | 404.30 | ufotable | Toho / Aniplex | 16 Oct 2020 |
| 2 | Sen to Chihiro no Kamikakushi | 316.80 | Studio Ghibli | Toho | 20 Jul 2001 |
| 3 | Kimi no Na wa. | 251.70 | CoMix Wave Films | Toho | 26 Aug 2016 |
| 4 | Mononoke Hime | 201.80 | Studio Ghibli | Toho | 12 Jul 1997 |
| 5 | One Piece Film: Red | 197.10 | Toei Animation | Toei | 6 Aug 2022 |
| 6 | Howl no Ugoku Shiro | 196.00 | Studio Ghibli | Toho | 20 Nov 2004 |
| 7 | Gake no Ue no Ponyo | 155.00 | Studio Ghibli | Toho | 19 Jul 2008 |
| 8 | Suzume no Tojimari | 147.90 | CoMix Wave Films | Toho | 11 Nov 2022 |
| 9 | The First Slam Dunk | 144.40 | Toei Animation / DandeLion Animation Studio | Toei | 3 Dec 2022 |
| 10 | Tenki no Ko | 142.30 | CoMix Wave Films | Toho | 19 Jul 2019 |
| 11 | Jujutsu Kaisen 0 Movie | 138.00 | MAPPA | Toho | 24 Dec 2021 |
| 12 | Detective Conan Movie: Kurogane no Submarine | 125.60 | TMS Entertainment | Toho | 14 Apr 2023 |
| 13 | Kaze Tachinu | 120.20 | Studio Ghibli | Toho | 20 Jul 2013 |
| 14 | Evangelion: 3.0+1.0 Thrice Upon a Time | 102.80 | Khara | Toho / Toei / Khara | 8 Mar 2021 |
| 15 | Detective Conan Movie: Halloween no Hanayome | 98.80 | TMS Entertainment | Toho | 12 Apr 2019 |
| 16 | Detective Conan Movie: The Fist of Blue Sapphire | 93.70 | TMS Entertainment | Toho | 12 Apr 2019 |
| 17 | Karigurashi no Arrietty | 92.50 | Studio Ghibli | Toho | 17 Jul 2010 |
| 18 | Detective Conan Movie: Zero the Enforcer | 91.80 | TMS Entertainment | Toho | 13 Apr 2018 |
| 19 | Stand By Me Doraemon | 83.80 | Shirogumi / Shin-Ei Animation | Toho | 8 Aug 2014 |
| 20 | Ged Senki | 78.40 | Studio Ghibli | Toho | 29 Jul 2006 |
| 21 | Youkai Watch Movie: Tanjou no Himitsu da Nyan! | 78.00 | OLM | Toho | 20 Dec 2014 |
| 22 | Detective Conan Movie: The Scarlet Bullet | 76.50 | TMS Entertainment | Toho | 16 Apr 2021 |
| 23 | Pokemon Movie: Mewtwo no Gyakushuu / Pikachu no Natsuyasumi | 72.40 | OLM | Toho | 18 Jul 1998 |
| 24 | Detective Conan Movie: The Crimson Love Letter | 68.90 | TMS Entertainment | Toho | 15 Apr 2017 |
| 25 | One Piece Film: Z | 68.70 | Toei Animation | Toei | 15 Dec 2012 |
| 26 | Ryuu to Sobakasu no Hime | 66.00 | Studio Chizu | Toho | 16 Jul 2021 |
| 27 | Neko no Ongaeshi | 64.80 | Studio Ghibli | Toho | 20 Jul 2002 |
| 28 | Pokemon Movie: Maboroshi no Pokemon Lugia Bakutan | 64.00 | OLM | Toho | 17 Jul 1999 |
| 29 | Detective Conan Movie: The Darkest Nightmare | 63.30 | TMS Entertainment | Toho | 16 Apr 2016 |
| 30 | Bakemono no Ko | 58.50 | Studio Chizu | Toho | 11 Jul 2015 |
| 31 | One Piece Movie: Stampede | 55.50 | Toei Animation | Toei | 9 Aug 2019 |
| 32 | Youkai Watch Movie: Enma Daiou to Itsutsu no Monogatari da Nyan! | 55.30 | OLM | Toho | 19 Dec 2015 |
| 33 | Kurenai no Buta | 54.00 | Studio Ghibli | Toho | 18 Jul 1992 |
| 34 | Doraemon Movie: Nobita no Takarajima | 53.70 | Shin-Ei Animation | Toho | 3 Mar 2018 |
| 35 | Evangelion: 3.0 You Can (Not) Redo | 53.00 | Khara | T Joy / Khara | 17 Nov 2012 |
| 36 | One Piece Film: Gold | 51.80 | Toei Animation | Toei | 23 Jul 2016 |
|
37
|
Pokemon Movie: Dialga vs. Palkia vs. Darkrai | 50.20 | OLM | Toho | 15 Jul 2007 |
| Doraemon Movie: Nobita no Getsumen Tansaki | 50.20 | Shin-Ei Animation | Toho | 1 Mar 2019 | |
| 39 | Pokemon Movie: Kesshoutou no Teiou Entei | 48.50 | OLM | Toho | 8 Jul 2000 |
|
40
|
Pokemon Movie: Giratina to Sora no Hanataba Sheimi | 48.00 | OLM | Toho | 19 Jul 2008 |
| One Piece Film: Strong World | 48.00 | Toei Animation | Toei | 12 Dec 2009 | |
| 41 | Pokemon Movie: Arceus Choukoku no Jikuu e | 46.70 | OLM | Toho | 18 Jul 2009 |
| 42 | Pokemon Movie: Nanayo no Negaiboshi Jirachi | 45.00 | OLM | Toho | 19 Jul 2003 |
| 43 | Detective Conan Movie: The Hellfire Sunflowers | 44.80 | TMS Entertainment | Toho | 18 Apr 2015 |
| 44 | Heisei Tanuki Gassen Ponpoko | 44.70 | Studio Ghibli | Toho | 13 Jun 1994 |
| 45 | Coquelicot-zaka kara | 44.60 | Studio Ghibli | Toho | 16 Jul 2011 |
| 46 | Doraemon Movie: Nobita no Nankyoku Kachikochi Daibouken | 44.30 | Shin-Ei Animation | Toho | 4 Mar 2017 |
| 47 | Pokemon Movie: Rekkuu no Houmonsha Deoxys | 43.80 | OLM | Toho | 17 Jul 2004 |
| 48 | Pokemon Movie Black: Victini to Shiroki Eiyuu Reshiram | 43.30 | Production I.G / Xebec / OLM | Toho | 16 Jul 2011 |
|
49
|
Majo no Takkyuubin | 43.00 | Studio Ghibli | Toho | 29 Jul 1989 |
| Pokemon Movie: Mew to Hadou no Yuusha Lucario | 43.00 | OLM | Toho | 16 Jul 2005 | |
| Doraemon Movie: Nobita to Sora no Utopia | 43.00 | Shin-Ei Animation | Toho | 3 Mar 2023 | |
| 51 | Lupin III vs. Detective Conan: The Movie | 42.60 | TMS Entertainment | Toho | 7 Dec 2013 |
| 52 | Ookami Kodomo no Ame to Yuki | 42.20 | Studio Chizu | Toho | 21 Jul 2012 |
| 53 | Pokemon Movie: Genei no Hasha Zoroark | 41.60 | OLM | Toho | 10 Jul 2010 |
| 54 | Doraemon Movie: Shin Nobita no Nippon Tanjou | 41.20 | Shin-Ei Animation | Toho | 5 Mar 2016 |
| 55 | Detective Conan Movie: The Sniper from Another Dimension | 41.10 | TMS Entertainment | Toho | 19 Apr 2014 |
| 56 | Kimetsu no Yaiba: Jougen Shuuketsu, Soshite Katanakaji no Sato e | 40.70 | ufotable | Toho / Aniplex | 3 Feb 2023 |
|
57
|
Evangelion: 2.0 You Can (Not) Advance | 40.00 | Khara | KlockWorx / Khara | 27 Jul 2009 |
| Dragon Ball Super: Broly | 40.00 | Toei Animation | Toei | 14 Dec 2018 | |
| 59 | Doraemon Movie: Nobita no Himitsu Dougu Museum | 39.80 | Shin-Ei Animation | Toho | 3 Mar 2013 |
| 60 | Doraemon Movie: Nobita no Space Heroes | 39.30 | Shin-Ei Animation | Toho | 7 Mar 2015 |
| 61 | Pokemon Movie: Celebi Toki wo Koeta Deai | 39.00 | OLM | Toho | 7 Jul 2001 |
| 62 | Dragon Ball Z Movie 15: Fukkatsu no “F” | 37.40 | Toei Animation | Toei / 20th Century Studios | 18 Apr 2015 |
| 63 | Detective Conan Movie: Private Eye in the Distant Sea | 36.30 | TMS Entertainment | Toho | 20 Apr 2013 |
| 64 | Doraemon Movie: Nobita to Kiseki no Shima – Animal Adventure | 36.20 | Shin-Ei Animation | Toho | 3 Mar 2012 |
| 65 | Pokemon Movie: Kyurem vs. Seikenshi | 36.10 | OLM | Toho | 14 Jul 2012 |
| 66 | Doraemon Movie: Shin Nobita no Daimakyou – Peko to 5-nin no Tankentai | 35.80 | Shin-Ei Animation | Toho | 8 Mar 2014 |
| 67 | Pokemon Movie 20: Kimi ni Kimeta! | 35.50 | OLM | Toho | 15 Jul 2017 |
| 68 | Doraemon Movie: Nobita no Shin Makai Daibouken – 7-nin no Mahoutsukai | 35.40 | Shin-Ei Animation | Toho | 10 Mar 2007 |
| 69 | Omoide no Marnie | 35.30 | Studio Ghibli | Toho | 19 Jul 2014 |
| 70 | Detective Conan Movie: The Raven Chaser | 35.00 | Tokyo Movie Shinsha | Toho | 18 Apr 2009 |
*Updated June 11, 2023
**More to be added soon