| Name | What | Region | Country | Lat | Long | Elev Ft. | Pop Est |
| Yadonou | city | Nagasaki-ken | Japan | 32.9 | 129.05 | 49 | 24144 |
| Yagami | city | Nagasaki-ken | Japan | 32.8666667 | 128.95 | 406 | 13997 |
| Yagami | city | Nagasaki-ken | Japan | 32.7666667 | 129.95 | 3 | 36032 |
| Yakami | city | Nagasaki-ken | Japan | 32.7666667 | 129.95 | 3 | 36032 |
| Yakezaki | city | Nagasaki-ken | Japan | 32.9333333 | 129 | 0 | 20394 |
| Yakisaki | city | Nagasaki-ken | Japan | 32.9333333 | 129 | 0 | 20394 |
| Yamanaka | city | Nagasaki-ken | Japan | 33.3333333 | 129.5 | 515 | 21744 |
| Yamashita | city | Nagasaki-ken | Japan | 32.5833333 | 128.75 | 3 | 7300 |
| Yamashitago | city | Nagasaki-ken | Japan | 32.5833333 | 128.75 | 3 | 7300 |
| Yamashitagō | city | Nagasaki-ken | Japan | 32.5833333 | 128.75 | 3 | 7300 |
| Yoguchi | city | Nagasaki-ken | Japan | 33.35 | 129.7166667 | 0 | 22445 |
| Yokose | city | Nagasaki-ken | Japan | 33.0833333 | 129.7 | 98 | 21849 |
| Yokoura | city | Nagasaki-ken | Japan | 34.3833333 | 129.3666667 | 275 | 26510 |
| Yoranain | city | Nagasaki-ken | Japan | 34.1030556 | 129.2236111 | 3 | 17392 |
| Yoranaīn | city | Nagasaki-ken | Japan | 34.1030556 | 129.2236111 | 3 | 17392 |
| Yoriki | city | Nagasaki-ken | Japan | 34.3166667 | 129.2166667 | 255 | 16621 |
| Yoshida | city | Nagasaki-ken | Japan | 34.4333333 | 129.3166667 | 282 | 29279 |
| Yoshigaura | city | Nagasaki-ken | Japan | 34.35 | 129.3666667 | 42 | 22183 |
| Yoshiishimo | city | Nagasaki-ken | Japan | 33.4166667 | 129.0716667 | 0 | 0 |
| Yotsugama | city | Nagasaki-ken | Japan | 32.9833333 | 129.65 | 190 | 22713 |
| Yuki | city | Nagasaki-ken | Japan | 32.8 | 130.0833333 | 26 | 33982 |
| Yukinoura | city | Nagasaki-ken | Japan | 32.9166667 | 129.6666667 | 314 | 34018 |
| Yunoki | city | Nagasaki-ken | Japan | 33.2 | 129.7666667 | 935 | 38222 |
| Yurugi | city | Nagasaki-ken | Japan | 32.9833333 | 129.7333333 | 164 | 36291 |
| Yuruki | city | Nagasaki-ken | Japan | 32.9833333 | 129.7333333 | 164 | 36291 |
| Yūki | city | Nagasaki-ken | Japan | 32.8 | 130.0833333 | 26 | 33982 |
|
|