| Skirt no Naka wa Kedamono Deshita | July 3, 2017 | — | — |
| Skull-face Bookseller Honda-san | October 8, 2018 | — | 12 |
| Sky Girls | — | — | — |
| Sky Girls | July 5, 2007 | Chiba Television Broadcasting | 26 |
| Sky Wizards Academy | July 8, 2015 | — | 12 |
| Skyers 5 | October 4, 1967 | — | 38 |
| Slam Dunk | October 16, 1993 | TV Asahi | 101 |
| Slap Up Party: Record of the Arad War | April 4, 2009 | — | 26 |
| Slayers | April 7, 1995 | — | 104 |
| Slayers Excellent | October 25, 1998 | — | 3 |
| Slayers Special | July 25, 1996 | — | 3 |
| Sleepy Princess in the Demon Castle | October 6, 2020 | AT-X, TV Tokyo, BS TV Tokyo | 12 |
| Slow Loop | January 7, 2022 | — | 12 |
| Slow Start | January 7, 2018 | Tokyo MX | 12 |
| Slow Step | June 1, 1991 | — | 5 |
| Smile Down the Runway | January 11, 2020 | — | 12 |
| Smile of the Arsnotoria the Animation | July 6, 2022 | — | 12 |
| Smile PreCure! | February 5, 2012 | — | 48 |
| Smoking Behind the Supermarket with You | July 10, 2026 | — | 12 |
| Smuggler | — | — | — |
| Snack Basue | January 13, 2024 | — | 13 |
| Snow White with the Red Hair | July 6, 2015 | — | 24 |
| Snowball Earth | April 3, 2026 | — | 13 |
| So I'm a Spider, So What? | January 8, 2021 | — | 24 |
| So What's Wrong with Getting Reborn as a Goblin? | October 5, 2026 | — | — |
| So, I Can't Play H? | July 6, 2012 | — | 12 |
| Soar High! Isami | April 8, 1995 | NHK Educational TV | 50 |
| Soara and the House of Monsters | 2027 | — | — |
| Soaring Sky! Pretty Cure | February 5, 2023 | TV Asahi | 50 |
| Sobakasu Pucchi | March 31, 1969 | Fuji Television | — |
| Soccer Fever | April 4, 1994 | NHK Satellite 2 Television | 51 |
| Softenni | April 8, 2011 | Tokyo MX | 12 |
| Sola | April 7, 2007 | — | 13 |
| Solo Camping for Two | July 11, 2025 | — | 24 |
| Solo Leveling | January 7, 2024 | — | 25 |
| Solty Rei | October 6, 2005 | TV Asahi | 24 |
| Somali and the Forest Spirit | January 9, 2020 | — | 12 |
| Someday's Dreamers | January 9, 2003 | — | 12 |
| Someday's Dreamers II: Sora | July 3, 2008 | — | 12 |
| Sometimes Even Reality Is a Lie! | 2027 | — | — |
| SoniAni: Super Sonico the Animation | January 6, 2014 | AT-X | 12 |
| Sonic Soldier Borgman | April 13, 1988 | — | 35 |
| Sonic X | April 6, 2003 | TV Tokyo | 78 |
| Sonny Boy | July 15, 2021 | — | 12 |
| Sono Toki, Kanojo wa. | October 7, 2018 | — | — |
| Sora no Manimani | July 7, 2009 | AT-X | 12 |
| Sora o Miageru Shōjo no Hitomi ni Utsuru Sekai | January 14, 2009 | — | 9 |
| Sorairo Utility | January 4, 2025 | — | 12 |
| Sorcerer Hunters | October 3, 1995 | TV Tokyo | 26 |
| Sorcerer Hunters OVA | December 21, 1996 | — | 3 |
| Sorcerous Stabber Orphen | October 3, 1998 | TBS Television | 47 |
| Sorcerous Stabber Orphen | January 7, 2020 | — | 48 |
| Soreike! Zukkoke San'ningumi | April 4, 2004 | TV Tokyo | 26 |
| Soul Buster | October 4, 2016 | — | 12 |
| Soul Eater | April 7, 2008 | Toku | 51 |
| Soul Eater Not! | April 8, 2014 | — | 12 |
| Soul Hunter | July 3, 1999 | TV Tokyo | 26 |
| Soul Link | April 11, 2006 | — | 12 |
| Sound of the Sky | January 4, 2010 | TV Tokyo | 12 |
| Sound! Euphonium | April 8, 2015 | — | 26 |