38 cities
| City | 2025 Pop. ↓ |
|---|---|
| Yokohama | 3,777,491 |
| Yono | 1,077,730 |
| Yokosuka | 428,992 |
| Yokkaichi | 295,841 |
| Yao | 273,213 |
| Yamagata | 254,538 |
| Yamaguchi | 145,515 |
| Yonago | 141,368 |
| Yaizu | 121,057 |
| Yonezawa | 94,486 |
| Yotsukaido | 86,701 |
| Yachimata | 83,322 |
| Yashio | 81,345 |
| Yawata | 71,656 |
| Yukuhashi | 71,277 |
| Yoshikawa | 60,510 |
| Yuki | 51,574 |
| Youkaichi | 45,338 |
| Yanagawa | 40,386 |
| Yokote | 39,178 |
| Yorii | 38,717 |
| Yaita | 36,275 |
| Yuzawa | 33,536 |
| Yokaichiba | 32,651 |
| Yamaga | 32,298 |
| Yanai | 32,229 |
| Yamoto | 32,028 |
| Yasugicho | 29,368 |
| Yugawara | 27,567 |
| Yoshii | 25,655 |
| Yoshida-kasugacho | 25,500 |
| Yamazakicho-nakabirose | 25,115 |
| Yoichi | 22,788 |
| Yatsuomachi-higashikumisaka | 22,205 |
| Yashiro | 21,554 |
| Yanagawamachi-saiwaicho | 20,807 |
| Yamada | 20,144 |
| Yuza | 17,082 |