| Sea KoalaPhantom Darkness · 037 | Phantom Darkness | 037 | Common | €0.07 |
| Sea LancerGeneration Force · 081 | Generation Force | 081 | Rare | $0.36 |
| Sealing Ceremony of KatonOrder of Chaos · 080 | Order of Chaos | 080 | Common | €0.07 |
| Sealing Ceremony of MokutonExtreme Victory · 077 | Extreme Victory | 077 | Common | €0.03 |
| Sealing Ceremony of RaitonGalactic Overlord · 078 | Galactic Overlord | 078 | Common | €0.09 |
| Sealing Ceremony of SuitonPhoton Shockwave · 080 | Photon Shockwave | 080 | Common | €0.04 |
| Sealmaster MeiseiAncient Sanctuary · 003 | Ancient Sanctuary | 003 | Rare | €0.10 |
| Seal of the AncientsYu-Gi-Oh! Power of Chaos: Kaiba the Revenge promotional cards · 003 | Yu-Gi-Oh! Power of Chaos: Kaiba the Revenge promotional cards | 003 | Prismatic Secret Rare | €1.65 |
| Seal of WickednessStardust Overdrive · 079 | Stardust Overdrive | 079 | Super Rare | €0.32 |
| Sea Lord's AmuletDuelist Saga · 009 | Duelist Saga | 009 | Ultra Rare | €0.25 |
| Seal, Strategist Fur HireDark Saviors · 018 | Dark Saviors | 018 | Super Rare | $0.20 |
| Sea Monster of TheseusRaging Tempest · 081 | Raging Tempest | 081 | Secret Rare | €0.26 |
| SearchlightmanEnemy of Justice · 010 | Enemy of Justice | 010 | Common | €0.10 |
| Search StrikerCrossroads of Chaos · 015 | Crossroads of Chaos | 015 | Rare | €0.04 |
| Searing Fire WallDuel Terminal 5a · 044 | Duel Terminal 5a | 044 | Duel Terminal Normal Parallel Rare | €0.20 |
| Sea Serpent Warrior of DarknessInvasion of Chaos · 059 | Invasion of Chaos | 059 | Common | €0.02 |
| Sea Stealth AttackLegendary Duelists · 018 | Legendary Duelists | 018 | Rare | €0.03 |
| Sea Stealth IILegendary Duelists: Duels From the Deep · 021 | Legendary Duelists: Duels From the Deep | 021 | Rare | €0.18 |
| Sebek's BlessingYu-Gi-Oh! Power of Chaos: Joey the Passion promotional cards · 002 | Yu-Gi-Oh! Power of Chaos: Joey the Passion promotional cards | 002 | Prismatic Secret Rare | €0.10 |
| Second BoosterThe Shining Darkness · 006 | The Shining Darkness | 006 | Common | €0.06 |
| Second Coin TossLegacy of Darkness · 083 | Legacy of Darkness | 083 | Rare | €1.17 |
| Second Expedition into Danger!Soul Fusion · 087 | Soul Fusion | 087 | Super Rare | €0.09 |
| Second GoblinMagician's Force · 013 | Magician's Force | 013 | Common | €0.02 |
| Secret BarrelMagician's Force · 046 | Magician's Force | 046 | Super Short Print | $0.98 |
| Secret BlastClash of Rebellions · 099 | Clash of Rebellions | 099 | Common | €0.09 |
| Secreterion DragonDuelist's Advance · 037 | Duelist's Advance | 037 | Ultra Rare | €0.36 |
| Secret Guards of the Ice BarrierDuel Terminal 4 · 083 | Duel Terminal 4 | 083 | Duel Terminal Normal Parallel Rare | €0.08 |
| Secret Pass to the TreasuresPharaonic Guardian · 037 | Pharaonic Guardian | 037 | Common | $0.17 |
| Secret PasswordGenesis Impact · 020 | Genesis Impact | 020 | Super Rare | €0.05 |
| Secret Sanctuary of the SpellcastersShadow Specters · 095 | Shadow Specters | 095 | Rare | €0.42 |
| Secret Sect Druid DruShadow Specters · 009 | Shadow Specters | 009 | Common | €0.05 |
| Secret Sect Druid WidShadow Specters · 008 | Shadow Specters | 008 | Common | €0.06 |
| Secret Six Samurai - DojiSpirit Warriors · 004 | Spirit Warriors | 004 | Secret Rare | €0.76 |
| Secret Six Samurai - FumaSpirit Warriors · 001 | Spirit Warriors | 001 | Secret Rare | €0.27 |
| Secret Six Samurai - GenbaSpirit Warriors · 002 | Spirit Warriors | 002 | Super Rare | €0.43 |
| Secret Six Samurai - HatsumeSpirit Warriors · 003 | Spirit Warriors | 003 | Secret Rare | €0.09 |
| Secret Six Samurai - KizaruSpirit Warriors · 005 | Spirit Warriors | 005 | Secret Rare | €0.14 |
| Secret Six Samurai - RihanSpirit Warriors · 006 | Spirit Warriors | 006 | Secret Rare | €3.78 |
| Secret Skills of the Six SamuraiSpirit Warriors · 007 | Spirit Warriors | 007 | Secret Rare | $0.84 |
| Secrets of Dark MagicLegendary Duelists: Magical Hero · 004 | Legendary Duelists: Magical Hero | 004 | Rare | $0.74 |
| Secrets of the GallantForce of the Breaker · 054 | Force of the Breaker | 054 | Common | $0.12 |
| Secret Village of the SpellcastersCrossroads of Chaos · 061 | Crossroads of Chaos | 061 | Super Rare | €0.02 |
| Sectarian of SecretsTournament Pack 8 · 019 | Tournament Pack 8 | 019 | Common | €0.27 |
| Secure GardnaExtreme Force · 043 | Extreme Force | 043 | Common | €0.11 |
| Security BlockCircuit Break · 053 | Circuit Break | 053 | Rare | €0.05 |
| Security DragonDuel Power · 037 | Duel Power | 037 | Ultra Rare | $0.20 |
| Security OrbGladiator's Assault · 089 | Gladiator's Assault | 089 | Ultra Rare | €0.13 |
| Security TokenUnlisted Printings | Unlisted Printings | — | — | — |
| Seed CannonCrimson Crisis · 057 | Crimson Crisis | 057 | Common | €0.06 |
| Seed of DeceptionCrossroads of Chaos · 046 | Crossroads of Chaos | 046 | Common | €0.10 |