| Ujishima | MSC-655 | 1942 | ex-USS Albatros class |
| Ukishima | MS-18/MSI-680 | 1945 | ex-IJN Pa-1 class |
| Ukishima | MSC-653 | 1980 | Hatsushima class |
| Ukushima | MSC-686 | 2001 | Sugashima class |
| Ume | PF-289 | 1943 | ex-USS Tacoma class |
| Umidori | PC-316 | 1962 | Mizutori class |
| Umigiri | DD-158 | 1989 | Asagiri class |
| Umitaka | PC-309 | 1959 | Umitaka class |
| Umitaka | PG-828 | 2003 | Hayabusa class |
| Umitsubame | MS-07/MSI-697 | 1943 | ex-IJN CHa-1 class |
| Unryu | SS-502 | 2008 | Soryu class |
| Uraga | MST-463 | 1996 | Uraga class |
| Uranami | DD-105 | 1957 | Ayanami class |
| Urume | MSC-626 | 1966 | Kasado class |
| Utone | MSC-633 | 1970 | Takami class |
| Utone | MST-475 | 1970 | Takami class |
| Uwajima | MSC-672 | 1990 | Uwajima class |
| Uzushio | SS-566 | 1970 | Uzushio class |
| Uzushio | SS-592 | 1998 | Oyashio class |
| Wakaba | DE-261 | 1945 | ex-IJN Tachibana class |
| Wakasa | AGS-5104 | 1985 | Futami class |
| Wakashio | SS-522 | 1961 | Hayashio class |
| Wakashio | SS-587 | 1993 | Harushio class |
| Wakataka | MS-83 | 1944 | ex-IJN CHa-1 class |
| Wakataka | PC-317 | 1962 | Umitaka class |
| Wakataka | PG-825 | 2001 | Hayabusa class |
| Washi | PC-304 | 1956 | Kari class |
| Yaeshio | SS-572 | 1977 | Uzushio class |
| Yaeshio | SS-598 | 2004 | Oyashio class |
| Yaeyama | MSO-301 | 1991 | Yaeyama class |
| Yaguruma | LSSL-450 | 1945? | ex-US LSSL type |
| Yakushima | MSC-658 | 1944 | ex-USS Albatros class |
| Yakushima | MSC-656 | 1982 | Hatsushima class |
| Yakushima | MCL-723 | 1982 | Hatsushima class |
| Yakushima | MSC-601 | 2007 | Hirashima class |
| Yamabato | MS-05 | 1944 | ex-IJN CHa-1 class |
| Yamabuki | LSSL-433 | 1945? | ex-US LSSL type |
| Yamadori | PC-312 | 1959 | Mizutori class |
| Yamagiku | LSSL-414 | 1945? | ex-US LSSL type |
| Yamagiri | DD-152 | 1987 | Asagiri class |
| Yamagumo | DD-113 | 1965 | Yamagumo class |
| Yamayuki | DD-129 | 1984 | Hatsuyuki class |
| Yamayuri | LSSL-437 | 1945? | ex-US LSSL type |
| Yashima | MSC-651 | 1953 | ex-US AMS type |
| Yashiro | MSC-603 | 1956 | Yashiro |
| Yokose | MSC-642 | 1975 | Takami class |
| Yoshikiri | MS-02/MSI-690 | 1944 | ex-IJN CHa-1 class |
| Yoshino | DE-223 | 1974 | Chikugo class |
| Yubari | DE-227 | 1982 | Yubari class |
| Yubetsu | DE-228 | 1983 | Yubari class |
| Yuchidori | MS-62/GP-445 | 1942 | ex-IJN 300t aircraft rescue craft |
| Yudachi | DD-108 | 1958 | Murasame class |
| Yudachi | DD-103 | 1997 | Murasame class (II) |
| Yukikaze | DD-102 | 1955 | Harukaze class |
| Yukishio | SS-581 | 1987 | Yushio class |
| Yugeshima | MSC-660 | 1944 | ex-USS Albatros class |
| Yugeshima | MSC-679 | 1996 | Uwajima class |
| Yugiri | DD-153 | 1987 | Asagiri class |
| Yugumo | DD-121 | 1977 | Yamagumo class |
| Yugure | DD-184 | 1943 | ex-USS Fletcher class |
| Yuhibari | MS-08 | 1944 | ex-IJN CHa-1 class |
| Yukari | MS-10/MSI-692 | 1944 | ex-IJN CHa-1 class |
| Yura | LSU-4171 | 1980 | Yura class |
| Yuri | LSSL-401 | 1945? | ex-US LSSL type |
| Yurishima | MSC-661 | 1944 | ex-USS Albatros class |
| Yurishima | MSC-668 | 1988 | Hatsushima class |
| Yushio | SS-573 | 1979 | Yushio class |
| Zuiryu | SS-505 | 2011 | Soryu class |