| Oosato observatory | Kumagaya | — |
| Ootake observatory | Ōtake | — |
| Osaki observatory | Ōsaki | — |
| Ray Observatory | Toyoura | — |
| Rikubetsu Astronomical Observatory | Prefectura de Hokkaido | — |
| Sakai Observatory | Sakai | — |
| Sakamoto Hachiryu Observatory | prefectura de Kumamoto | — |
| Sakamoto Observatory | Ōtsu | — |
| Saku observatory | Saku | — |
 Sakurajima Volcano Research Center | Sakurajima Yokoyama-chō | — |
 Sapporo Astronomical Observatory | Chūō-ku | — |
 Sapporo Science Center | Sapporo | — |
| Seiwa Kogen Observatory | — | — |
 Sendai Astronomical Observatory | Nishikigaoka | 163 m |
| Sendai Astronomical Observatory Ayashi Station | Shimoayashi | — |
| Sendai Municipal Observatory | Sendai | — |
 Sendai Space Museum | Nagatoshi-chō | — |
| Sengamine Observatory | Kami | — |
| Shimada observatory | Shimada | — |
| Shimotsuma observatory | Shimotsuma | — |
| Shinshiro observatory | Aichi Prefectural Xincheng East High School | — |
| Shishikui observatory | Shishikui | — |
| Shizuoka observatory | Shizuoka | — |
 Shosanbetsu observatory | Prefectura de Hokkaido | — |
| Southern Utsunomiya observatory | Utsunomiya | — |
| Space Tracking and Communications Center, JAXA | Ibara | — |
 Star Square Astronomical Observatory | Shimizu-ku | — |
| STARS-AO | — | — |
| Sukagawa observatory | Sukagawa | — |
| Sumoto observatory | Sumoto | — |
| Suntopia Marina observatory | Sumoto | — |
 Super-Kamiokande | Hida | — |
| Tachibana Observatory | Miyakonojō | — |
| Tajimi observatory | Tajimi | — |
| Takanezawa observatory | Takanezawa | — |
 Tochigi Science Museum | Utsunomiya | — |
| Tokai observatory | Tōkai | — |
| Tokigawa Town Star and Green Creation Center | Tokigawa | — |
| Tokushima observatory | Tokushima | — |
| Tokyo Astronomical Observatory (before 1938) | Tokio | — |
| Tokyo-Asahikawa observatory | Tokio | — |
| Tokyo-Dodaira observatory | Tokio | — |
| Tokyo-Mitaka observatory | Tokio | — |
| Tokyo-Norikura observatory | Tokio | — |
| Tokyo-Okayama observatory | Tokio | — |
| Toma observatory | Toma | — |
| Tosa observatory | Tosa | — |
 Toyama City Observatory | Prefectura de Toyama | — |