This is a list of all the ultra-prominent peaks (with topographic prominence greater than 1,500 metres) in Japan.
| No | Peak | Island | Elevation (m) | Prominence (m) | Col (m) |
|---|---|---|---|---|---|
| 1 | Mount Fuji | Honshū | 3,776 | 3,776 | 0 |
| 2 | Mount Hotaka | Honshū | 3,190 | 2,307 | 883 |
| 3 | Asahidake | Hokkaidō | 2,290 | 2,290 | 0 |
| 4 | Mount Kita | Honshū | 3,192 | 2,239 | 953 |
| 5 | Mount Ishizuchi | Shikoku | 1,982 | 1,982 | 0 |
| 6 | Mount Miyanoura | Yakushima | 1,936 | 1,936 | 0 |
| 7 | Mount Aka | Honshū | 2,899 | 1,916 | 883 |
| 8 | Mount Haku | Honshū | 2,702 | 1,897 | 805 |
| 9 | Mount Chōkai | Honshū | 2,236 | 1,891 | 345 |
| 10 | Mount Yōtei | Hokkaidō | 1,898 | 1,878 | 20 |
| 11 | Mount Kujū | Kyūshū | 1,791 | 1,791 | 0 |
| 12 | Mount Kisokoma | Honshū | 2,956 | 1,751 | 1205 |
| 13 | Mount Iwate | Honshū | 2,038 | 1,745 | 293 |
| 14 | Mount Hakkyō | Honshū | 1,915 | 1,732 | 183 |
| 15 | Mount Rishiri | Rishiri Island | 1,721 | 1,721 | 0 |
| 16 | Mount Ontake | Honshū | 3,067 | 1,712 | 1355 |
| 17 | Mount Hiuchi | Honshū | 2,462 | 1,637 | 825 |
| 18 | Daisen | Honshū | 1,729 | 1,634 | 95 |
| 19 | Mount Nikkō-Shirane | Honshū | 2,578 | 1,613 | 965 |
| 20 | Mount Dainichi | Honshū | 2,128 | 1,593 | 535 |
| 21 | Mount Tsurugi | Shikoku | 1,955 | 1,540 | 415 |
