| Seed of FlameCrossroads of Chaos · 081 | Crossroads of Chaos | 081 | Ultra Rare | €0.14 |
| Seed-Spitting SaplingsAge of Overlord · 022 | Age of Overlord | 022 | Super Rare | €0.06 |
| Seed TokenUnlisted Printings | Unlisted Printings | — | — | — |
| Segmental DragonStructure Deck: Powercode Link · 008 | Structure Deck: Powercode Link | 008 | Ultra Rare | $0.20 |
| Seismic CrasherForce of the Breaker · 027 | Force of the Breaker | 027 | Common | €0.02 |
| Seismic ShockwaveStructure Deck: Dinosaur's Rage · 031 | Structure Deck: Dinosaur's Rage | 031 | Common | €0.09 |
| SeiyaryuYu-Gi-Oh! Dark Duel Stories promotional cards · 004 | Yu-Gi-Oh! Dark Duel Stories promotional cards | 004 | Prismatic Secret Rare | €0.22 |
| Sekka's LightFlames of Destruction · 062 | Flames of Destruction | 062 | Rare | $0.28 |
| Seleglare the Luminous Lunar DragonRise of the Duelist · 087 | Rise of the Duelist | 087 | Ultra Rare | $0.26 |
| Selene, Queen of the Master MagiciansDuel Overload · 014 | Duel Overload | 014 | Ultra Rare | €0.14 |
| Selettrice VaalmonicaLegacy of Destruction · 022 | Legacy of Destruction | 022 | Ultra Rare | €0.63 |
| Self-Destruct AntCircuit Break · 035 | Circuit Break | 035 | Common | €0.08 |
| Self-Destruct ButtonInvasion of Chaos · 105 | Invasion of Chaos | 105 | Short Print | €0.05 |
| Self-MummificationExtreme Victory · 062 | Extreme Victory | 062 | Common | €0.16 |
| Senet SwitchCyberdark Impact · 048 | Cyberdark Impact | 048 | Common | €0.05 |
| SengenjinYu-Gi-Oh! World Championship 2004 prize cards · 403 | Yu-Gi-Oh! World Championship 2004 prize cards | 403 | Super Rare | €0.02 |
| Sengenjin Wakes from a MillenniumThe Infinite Forbidden · 001 | The Infinite Forbidden | 001 | Ultra Rare | $3.87 |
| Senior Silver NinjaPhoton Shockwave · 031 | Photon Shockwave | 031 | Common | €0.11 |
| Senju of the Thousand HandsMagic Ruler · 080 | Magic Ruler | 080 | Rare | €0.08 |
| Senko the Skybolt StarBattles of Legend: Crystal Revenge · 036 | Battles of Legend: Crystal Revenge | 036 | Ultra Rare | €0.08 |
| Senri EyeMagician's Force · 089 | Magician's Force | 089 | Common | €0.03 |
| Sentence of DoomLegendary Duelists: Immortal Destiny · 005 | Legendary Duelists: Immortal Destiny | 005 | Super Rare | $0.17 |
| Sentinel of the SeasChampion Pack: Game Six · 012 | Champion Pack: Game Six | 012 | Common | €0.56 |
| Sentinel of the TistinaUnlisted Printings | Unlisted Printings | — | — | €0.16 |
| Sentry Soldier of StoneYu-Gi-Oh! The Dark Side of Dimensions Movie Pack · 012 | Yu-Gi-Oh! The Dark Side of Dimensions Movie Pack | 012 | Ultra Rare | $0.12 |
| Sephylon, the Ultimate TimelordShonen Jump December 2011 subscription bonus · 054 | Shonen Jump December 2011 subscription bonus | 054 | Ultra Rare | $0.25 |
| Seraphim PapillionChaos Impact · 050 | Chaos Impact | 050 | Common | €0.10 |
| Serenade the Melodious DivaThe New Challengers · 005 | The New Challengers | 005 | Common | €0.12 |
| Serene Psychic GirlDuelist's Advance · 013 | Duelist's Advance | 013 | Common | €0.08 |
| Serene Psychic SorceressDoom of Dimensions · 042 | Doom of Dimensions | 042 | Common | €0.08 |
| Serene Psychic WitchExtreme Victory · 026 | Extreme Victory | 026 | Common | €0.10 |
| Sergeant ElectroPhoton Shockwave · 090 | Photon Shockwave | 090 | Ultra Rare | €0.05 |
| Serial SpellRise of Destiny · 037 | Rise of Destiny | 037 | Rare | €0.92 |
| Serpentine PrincessLegacy of Darkness · 057 | Legacy of Darkness | 057 | Common | €0.07 |
| Serpent MarauderUnlisted Printings | Unlisted Printings | — | — | — |
| Serpent Night DragonMagic Ruler · 103 | Magic Ruler | 103 | Secret Rare | €0.02 |
| Serpent SuppressionAbsolute Powerforce · 066 | Absolute Powerforce | 066 | Common | €0.08 |
| Servant of CatabolismPharaonic Guardian · 012 | Pharaonic Guardian | 012 | Common | $0.18 |
| Servant of EndymionStructure Deck: Order of the Spellcasters · 004 | Structure Deck: Order of the Spellcasters | 004 | Common | €0.38 |
| Servants of the Fallen KingSpeed Duel: Scars of Battle · 04 | Speed Duel: Scars of Battle | 04 | Super Rare | €0.57 |
| Service Puppet PlayThe Infinite Forbidden · 070 | The Infinite Forbidden | 070 | Common | €0.09 |
| Serziel, Watcher of the Evil EyeThe Infinity Chasers · 027 | The Infinity Chasers | 027 | Secret Rare | $0.39 |
| Set RotationMaximum Crisis · 064 | Maximum Crisis | 064 | Short Print | €0.07 |
| Setting SunSpeed Duel GX: Duelists of Shadows · 14 | Speed Duel GX: Duelists of Shadows | 14 | Common | $0.05 |
| SetuppercutRising Rampage · 078 | Rising Rampage | 078 | Common | €0.04 |
| Seven Cities of the Golden LandBlazing Vortex · 062 | Blazing Vortex | 062 | Ultra Rare | $1.42 |
| Seven Stars Slash - Army Annihilator HagunAlliance Insight · 069 | Alliance Insight | 069 | Common | €0.04 |
| Seven Swords WarriorShonen Jump December 2010 subscription bonus · 047 | Shonen Jump December 2010 subscription bonus | 047 | Ultra Rare | €0.22 |
| Seventh AscensionLegendary Duelists: Duels From the Deep · 006 | Legendary Duelists: Duels From the Deep | 006 | Ultra Rare | €0.17 |
| Seventh EternityLegendary Duelists: Duels From the Deep · 007 | Legendary Duelists: Duels From the Deep | 007 | Rare | $0.19 |