| Yoshinaga-san Chi no Gargoyle | April 4, 2006 | — | 13 |
| Yosuga no Sora | October 4, 2010 | — | 12 |
| Yotsunoha | February 29, 2008 | — | 2 |
| You and I Are Polar Opposites | January 11, 2026 | — | 25 |
| You and Idol Pretty Cure | February 2, 2025 | All-Nippon News Network, TV Asahi | — |
| You Are Ms. Servant | October 6, 2024 | — | 12 |
| You Can't Be in a Rom-Com with Your Childhood Friends! | January 6, 2026 | — | 12 |
| You Don't Know Gunma Yet | April 2, 2018 | — | 12 |
| You Were Experienced, I Was Not: Our Dating Story | October 6, 2023 | — | 12 |
| You're Under Arrest | October 5, 1996 | TBS Television | — |
| You're Under Arrest | — | — | — |
| Young Black Jack | October 1, 2015 | TBS Television | 12 |
| Young Ladies Don't Play Fighting Games | July 7, 2026 | — | 12 |
| Your Forma | April 2, 2025 | — | 13 |
| Your Lie in April | October 9, 2014 | — | 22 |
| Yowamushi Pedal | October 7, 2013 | TV Tokyo | — |
| Yowayowa Sensei | April 11, 2026 | — | 12 |
| Yozakura Quartet | October 2, 2008 | — | 12 |
| Yozakura Quartet: Hana no Uta | October 6, 2013 | — | 13 |
| Yozakura Quartet: Hoshi no Umi | October 8, 2010 | — | 3 |
| Yozakura Quartet: Tsuki ni Naku | October 9, 2013 | — | 3 |
| Ys | November 21, 1989 | — | 7 |
| Ys II: Castle in the Heavens | December 16, 1992 | — | 4 |
| Yu Yu Hakusho | October 10, 1992 | Fuji Television | 112 |
| Yu-Gi-Oh! | April 4, 1998 | TV Asahi | 27 |
| Yu-Gi-Oh! 5D's | April 2, 2008 | TV Tokyo | 154 |
| Yu-Gi-Oh! Arc-V | April 6, 2014 | — | 148 |
| Yu-Gi-Oh! Capsule Monsters | September 9, 2006 | — | 12 |
| Yu-Gi-Oh! Duel Monsters | April 18, 2000 | TV Tokyo | 224 |
| Yu-Gi-Oh! Go Rush!! | April 3, 2022 | TV Tokyo | — |
| Yu-Gi-Oh! GX | October 6, 2004 | TV Tokyo | 180 |
| Yu-Gi-Oh! Sevens | April 4, 2020 | TV Tokyo | 92 |
| Yu-Gi-Oh! VRAINS | May 10, 2017 | TV Tokyo | 120 |
| Yu-Gi-Oh! Zexal | April 11, 2011 | TV Tokyo | 146 |
| Yugo the Negotiator | February 24, 2004 | Kids Station | 13 |
| Yuki Yuna is a Hero | October 17, 2014 | — | 36 |
| Yukikaze | August 28, 2002 | — | 5 |
| Yume Miru, Anime: On-chan | January 18, 2008 | Hokkaido Television Broadcasting | 52 |
| Yume no Crayon Oukoku | September 7, 1997 | — | 70 |
| Yume Tsukai | April 8, 2006 | — | 12 |
| Yumeiro Patissiere | October 4, 2009 | Nippon Television | 63 |
| Yumeria | January 8, 2004 | — | 12 |
| Yurayura Q | — | — | — |
| Yurei Deco | July 3, 2022 | — | — |
| Yuri Is My Job! | April 6, 2023 | — | 12 |
| Yuri on Ice | October 6, 2016 | TV Asahi | 12 |
| Yuri-gami Sama ga Miteru | January 29, 2022 | YouTube | — |
| Yurikuma Arashi | January 5, 2015 | — | 12 |
| Yurumates 3D | April 2, 2012 | — | 26 |
| YuruYuri | July 5, 2011 | AT-X | 36 |
| Yuruyuru Zukan | October 4, 2026 | — | — |
| Yuuna and the Haunted Hot Springs | July 14, 2018 | — | 12 |
| Yuuyake Banchō | September 30, 1968 | Nippon Television | 26 |
| Yuyushiki | April 9, 2013 | — | 12 |
| Yōkai Ningen Bem | October 7, 1968 | Fuji Television | — |
| Yōkai Ningen Bem | April 1, 2006 | — | 26 |
| Yōkaiden Nekome Kozō | April 1, 1976 | TV Tokyo | — |
| Yōtōden | — | — | — |
| Yūkan Club | July 25, 1991 | — | 2 |
| Yūsanchi! from Yū-hachi | October 5, 2026 | Fuji Television | — |