| Yadamon - Wonderland Dreams | Super Nintendo Entertainment System | 1993 | — |
| Yae | Super Nintendo Entertainment System | 1996 | Konami |
| Yakuman | Game Boy | 1989 | Intelligent Systems |
| Yakuman Houou | Nintendo 3DS | 2015 | Lancarse, Nintendo |
| Yakōchū | Super Nintendo Entertainment System | 1995 | Athena |
| Yamaha Supercross | Wii | 2008 | Beyond Reality Games |
| Yeti3DS | Nintendo 3DS | — | smealum |
| Yie Ar Kung-Fu | Nintendo Entertainment System | 1985 | Konami |
| Yo! Noid | Nintendo Entertainment System | 1990 | Now Production |
| Yo-kai Watch | Nintendo 3DS | 2013 | Level-5 |
| Yo-kai Watch 2 | Nintendo 3DS | 2014 | Level-5 |
| Yo-kai Watch 2: Bony Spirits | Nintendo 3DS | 2014 | Level-5 |
| Yo-kai Watch 2: Fleshy Souls | Nintendo 3DS | 2014 | Level-5 |
| Yo-kai Watch 2: Psychic Specters | Nintendo 3DS | 2014 | Level-5 |
| Yo-kai Watch 3 | Nintendo 3DS | 2016 | Level-5 |
| Yo-kai Watch Blasters | Nintendo 3DS | 2015 | Level-5 |
| Yo-kai Watch Blasters 2 | Nintendo 3DS | 2017 | Level-5 |
| Yoga Wii | Wii | 2009 | Trine Games |
| Yogi Bear's Gold Rush | Game Boy | 1994 | — |
| Yogi Bear: The Video Game | Wii | 2010 | Vicious Cycle Software |
| Yokai Club | Nintendo Entertainment System | 1987 | Tose Co. |
| Yokai Dochuki | Nintendo Entertainment System | 1987 | Namco |
| Yokoyama Mitsuteru Sangokushi | Super Nintendo Entertainment System | 1992 | — |
| Yokozuna Monogatari | Super Nintendo Entertainment System | 1994 | — |
| Yoshi | Nintendo Entertainment System, Game Boy | 1991 | Game Freak |
| Yoshi no Cookie: Kuruppon Oven de Cookie | Super Nintendo Entertainment System | 1994 | — |
| Yoshi Racing | Super Nintendo Entertainment System | — | Argonaut Games |
| Yoshi's Cookie | Nintendo Entertainment System, Super Nintendo Entertainment System, Game Boy | 1992 | Bullet-Proof Software, Tose Co. |
| Yoshi's New Island | Nintendo 3DS | 2014 | Arzest |
| Yoshi's Safari | Super Nintendo Entertainment System | 1993 | Nintendo Research & Development 1 |
| Yoshi's Woolly World | Nintendo 3DS | 2015 | Good-Feel |
| You Don't Know Jack | Wii | 2011 | Jackbox Games |
| You, Me, and the Cubes | Wii | 2009 | D Wonderland Inc., fyto |
| Young Merlin | Super Nintendo Entertainment System | 1994 | Westwood Studios |
| Your Shape | Wii | 2009 | Ubisoft |
| Ys I | Nintendo Entertainment System | 1987 | Nihon Falcom |
| Ys I & II | Wii | 1989 | Nihon Falcom, Alfa System |
| Ys II | Nintendo Entertainment System | 1988 | Nihon Falcom |
| Ys III: Wanderers from Ys | Nintendo Entertainment System, Super Nintendo Entertainment System | 1989 | Nihon Falcom |
| Ys IV: Mask of the Sun | Super Nintendo Entertainment System | 1993 | Tonkin House |
| Ys V: Lost Kefin, Kingdom of Sand | Super Nintendo Entertainment System | 1995 | Nihon Falcom |
| Yu Yu Hakusho | Game Boy | 1993 | — |
| Yu Yu Hakusho | Super Nintendo Entertainment System | 1993 | — |
| Yu-Gi-Oh! 5D's Duel Transer | Wii | 2010 | Konami Digital Entertainment |
| Yu-Gi-Oh! 5D's Wheelie Breakers | Wii | 2009 | Konami |
| Yu-Gi-Oh! The Falsebound Kingdom | Nintendo GameCube | 2002 | Konami |
| Yu-Gi-Oh! Zexal: World Duel Carnival | Nintendo 3DS | 2014 | — |
| Yume Penguin Monogatari | Nintendo Entertainment System | 1991 | Konami |
| Yummy Yummy Cooking Jam | Wii | 2008 | Virtual Toys |
| Yuujin no Furi Furi Girls | Super Nintendo Entertainment System | 1994 | — |
| Yū Yū Hakusho Final | Super Nintendo Entertainment System | 1995 | Tose Co. |
| Yūyu no Quiz de Go! Go! | Super Nintendo Entertainment System | 1991 | — |