| Shinobanai! CryptoNinja Sakuya | October 4, 2023 | — | — |
| Shinobi no Ittoki | October 4, 2022 | — | 12 |
| Shinshō Genmukan | March 20, 2010 | — | 4 |
| Shinsū Sudama-hen | October 12, 1988 | — | 4 |
| Shinya! Tensai Bakabon | July 10, 2018 | TV Tokyo | 12 |
| Shinzo | February 5, 2000 | — | 32 |
| Shion no Ō | October 13, 2007 | Fuji Television | 22 |
| Shippū! Iron Leaguer | April 6, 1993 | — | 52 |
| Shippū! Iron Leaguer Ginhikari no Hata no Shita ni | November 21, 1994 | — | — |
| Shirobako | October 9, 2014 | Tokyo MX | 24 |
| Shirogane no Ishi Argevollen | July 3, 2014 | — | — |
| Shironeko Project: Zero Chronicle | April 6, 2020 | — | 12 |
| Shogun in His Boyhood | April 9, 1975 | — | 20 |
| Shokupan Mimi | October 4, 2010 | — | 10 |
| Shomin Sample | October 7, 2015 | — | 12 |
| Shonen Ashibe Go! Go! Goma-chan | April 5, 2016 | — | 120 |
| Shoot! | November 7, 1993 | Fuji Television | 58 |
| Show by Rock!! | April 5, 2015 | — | 12 |
| Shrine of the Morning Mist | July 4, 2002 | — | 26 |
| Shuffle! | July 7, 2005 | WOWOW | 24 |
| Shugo Chara! | October 6, 2007 | TV Tokyo | 127 |
| Shukufuku no Campanella | July 2, 2010 | — | 12 |
| Shura ga Yuku | — | — | — |
| Shuudengo, Capsule Hotel de, Joushi ni Binetsu Tsutawaru Yoru. | October 8, 2018 | Tokyo MX | 12 |
| Shy | October 3, 2023 | — | 24 |
| Shō 3 Ashibe QQ Goma-chan | April 12, 2026 | TV Tokyo | — |
| Shōjo Sect | — | — | — |
| Shōjo-tachi no Sadism | September 2, 2016 | — | 2 |
| Shōnan Bakusōzoku | — | — | — |
| Shōnen Ashibe | January 21, 1991 | — | 6 |
| Shōnen Ashibe | April 11, 1991 | TBS Television | 62 |
| Shōnen Hollywood | — | — | — |
| Shōnen Maid | April 8, 2016 | — | 12 |
| Shōnen Ninja Kaze no Fujimaru | June 7, 1964 | — | 65 |
| Shōnen Onmyōji | October 3, 2006 | Kansai Telecasting Corporation | 26 |
| Shōwa Ahō Zhoshi Akanuke Ichiban! | October 7, 1985 | — | 22 |
| Shōwa Genroku Rakugo Shinjū | January 9, 2016 | — | — |
| Shōwa Monogatari | April 4, 2011 | — | — |
| Shōzen | April 2027 | — | — |
| Shūkan Ranobe Anime | July 13, 2025 | — | 12 |
| Si-Vis: The Sound of Heroes | October 5, 2025 | — | — |
| Silent Möbius | April 7, 1998 | TV Tokyo | 26 |
| Silkroad Kids Yuto | September 16, 2006 | NHK Satellite 2 Television | 26 |
| Silver Fang | April 7, 1986 | TV Asahi | 21 |
| Silver Spoon | July 12, 2013 | — | 22 |
| Simoun | April 3, 2006 | — | 26 |
| Sin cara 2.0 | September 27, 1991 | — | 2 |
| Sing "Yesterday" for Me | April 4, 2020 | — | 12 |
| Sirius the Jaeger | July 12, 2018 | AT-X | 12 |
| Sirotan | October 3, 2026 | — | — |
| Sister Princess | April 4, 2001 | — | 26 |
| Sister Princess RePure | April 4, 2001 | — | — |
| Sisters of Wellber | April 3, 2007 | — | 26 |
| SK8 the Infinity | January 10, 2021 | — | 12 |
| Skate-Leading Stars | January 10, 2021 | — | 12 |
| Skeleton Knight in Another World | April 7, 2022 | — | 12 |
| Sket Dance | April 7, 2011 | TV Tokyo | 77 |
| Sketchbook ~full color's~ | October 2, 2007 | TV Tokyo | 13 |
| Skip and Loafer | April 4, 2023 | NHK General TV | 12 |
| Skip Beat! | October 5, 2008 | — | 25 |