| Yang Zing PranaDuelist Alliance · 062 | Duelist Alliance | 062 | Common | €0.05 |
| Yang Zing UnleashedDuelist Alliance · 075 | Duelist Alliance | 075 | Common | €0.09 |
| YaranzoMcDonald's Promotional Cards · 005 | McDonald's Promotional Cards | 005 | Common | $1.35 |
| Yasha, the Skeletal MayakashiHidden Summoners · 031 | Hidden Summoners | 031 | Super Rare | €0.24 |
| YashinokiUnlisted Printings | Unlisted Printings | — | — | — |
| Yata-GarasuLegacy of Darkness · 000 | Legacy of Darkness | 000 | Secret Rare | €0.08 |
| Yazi, Evil of the Yang ZingThe New Challengers · 051 | The New Challengers | 051 | Ultimate Rare | €0.18 |
| Y-Dragon HeadMagician's Force · 005 | Magician's Force | 005 | Super Rare | €0.15 |
| Yellow Baboon, Archer of the ForestStardust Overdrive · 084 | Stardust Overdrive | 084 | Ultra Rare | $1.59 |
| Yellow-Bellied OniShadow Specters · 033 | Shadow Specters | 033 | Common | $0.06 |
| Yellow Dragon NinjaShadows in Valhalla · 013 | Shadows in Valhalla | 013 | Secret Rare | €0.33 |
| Yellow DustonJudgment of the Light · 040 | Judgment of the Light | 040 | Short Print | $0.21 |
| Yellow GadgetStructure Deck: Machine Re-Volt · 008 | Structure Deck: Machine Re-Volt | 008 | Common | €0.04 |
| Yellow Luster ShieldInvasion of Chaos · 037 | Invasion of Chaos | 037 | Common | €0.05 |
| Yellow NinjaShadows in Valhalla · 012 | Shadows in Valhalla | 012 | Super Rare | €0.05 |
| Yoa the Plague AshtraBeyond the Brave · 011 | Beyond the Brave | 011 | Common | €0.09 |
| Yoko, the Graceful MayakashiHidden Summoners · 035 | Hidden Summoners | 035 | Secret Rare | $4.22 |
| YokotunerInvasion: Vengeance: Special Edition · 4 | Invasion: Vengeance: Special Edition | 4 | Super Rare | €0.09 |
| Yoko-Zuna Sumo SpiritExtreme Force · 000 | Extreme Force | 000 | Common | €0.04 |
| Yomagna the Fire PhantomChaos Origins · 083 | Chaos Origins | 083 | Common | €0.09 |
| Yomi ShipPharaonic Guardian · 071 | Pharaonic Guardian | 071 | Common | €0.13 |
| Yorishiro of the AquaDarkwing Blast · 092 | Darkwing Blast | 092 | Common | €0.07 |
| YormungardeUnlisted Printings | Unlisted Printings | — | — | — |
| Yosenju IznaRising Rampage · 010 | Rising Rampage | 010 | Common | €0.03 |
| Yosenju Kama 1The Secret Forces · 003 | The Secret Forces | 003 | Secret Rare | $0.15 |
| Yosenju Kama 2The Secret Forces · 004 | The Secret Forces | 004 | Secret Rare | $0.18 |
| Yosenju Kama 3The Secret Forces · 005 | The Secret Forces | 005 | Secret Rare | €0.19 |
| Yosenju KodamCrossed Souls · 018 | Crossed Souls | 018 | Common | €0.08 |
| Yosenju MagatSecrets of Eternity · 026 | Secrets of Eternity | 026 | Common | €0.08 |
| Yosenju MisakThe Secret Forces · 002 | The Secret Forces | 002 | Secret Rare | €0.17 |
| Yosenju Oroshi ChannelingRising Rampage · 092 | Rising Rampage | 092 | Common | €0.13 |
| Yosenju OyamCrossed Souls · 019 | Crossed Souls | 019 | Rare | €0.14 |
| Yosenju SabuRising Rampage · 009 | Rising Rampage | 009 | Common | €0.04 |
| Yosenju Shinchu LThe Secret Forces · 006 | The Secret Forces | 006 | Super Rare | €0.14 |
| Yosenju Shinchu RThe Secret Forces · 007 | The Secret Forces | 007 | Super Rare | $0.09 |
| Yosenjus' Secret MoveThe Secret Forces · 009 | The Secret Forces | 009 | Super Rare | $0.11 |
| Yosenjus' Sword StingRising Rampage · 071 | Rising Rampage | 071 | Common | €0.05 |
| Yosenju TsujikSecrets of Eternity · 027 | Secrets of Eternity | 027 | Common | $0.11 |
| Yosenju Wind WorshipRising Rampage · 057 | Rising Rampage | 057 | Common | €0.08 |
| Yosen Training GroundsThe Secret Forces · 008 | The Secret Forces | 008 | Super Rare | $0.08 |
| Yosen WhirlwindCrossed Souls · 058 | Crossed Souls | 058 | Common | $0.11 |
| You and A.I.Lightning Overdrive · 061 | Lightning Overdrive | 061 | Common | €0.05 |
| You're FinishedDuelist Nexus · 080 | Duelist Nexus | 080 | Super Rare | €0.16 |
| You're in Danger!Dark Neostorm · 085 | Dark Neostorm | 085 | Rare | €0.07 |
| YowieBrothers of Legend · 007 | Brothers of Legend | 007 | Secret Rare | $0.21 |
| YubelPhantom Darkness · 006 | Phantom Darkness | 006 | Super Rare | €1.71 |
| Yubel - Terror IncarnatePhantom Darkness · 007 | Phantom Darkness | 007 | Ultra Rare | €0.93 |
| Yubel - The Loving Defender ForeverPhantom Nightmare · 038 | Phantom Nightmare | 038 | Ultra Rare | €1.28 |
| Yubel - The Ultimate NightmarePhantom Darkness · 008 | Phantom Darkness | 008 | Secret Rare | $0.76 |
| Yu-Jo FriendshipShonen Jump May 2006 subscription bonus · 007 | Shonen Jump May 2006 subscription bonus | 007 | Ultra Rare | €77.47 |