Ten years after the Ceremonial Battle, a teenage boy named Yuuki Judai heads off in order to join the Duelist Yousei School located on a remote island off the coast of Japan. There he meets his fellow students and gains a few friends, along with a few enemies. Judai is put into the lowest rank of Osiris Red, but he continues to test his skills against the students and faculty to prove his worth as a Yousei Duelist and earn the respect of everyone around him.
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| Title | Air Date | Duration | ||
|---|---|---|---|---|
| Season 1 | Episode 1 | The Next King of Games | 2004-10-06 | 25 min |
| Season 1 | Episode 2 | Welcome to Duel Academy | 2004-10-13 | 25 min |
| Season 1 | Episode 3 | A Duel in Love | 2004-10-20 | 25 min |
| Season 1 | Episode 4 | Raring to Go | 2004-10-27 | 25 min |
| Season 1 | Episode 5 | The Shadow Duelist (1) | 2004-11-03 | 25 min |
| Season 1 | Episode 6 | The Shadow Duelist (2) | 2004-11-10 | 25 min |
| Season 1 | Episode 7 | Duel and Unusual Punishment | 2004-11-17 | 25 min |
| Season 1 | Episode 8 | For the Sake of Syrus | 2004-11-24 | 25 min |
| Season 1 | Episode 9 | Family Business | 2004-12-01 | 25 min |
| Season 1 | Episode 10 | Tag Team Trial (1) | 2004-12-08 | 25 min |
| Season 1 | Episode 11 | Tag Team Trial (2) | 2004-12-15 | 25 min |
| Season 1 | Episode 12 | Formula for Success | 2004-12-22 | 25 min |
| Season 1 | Episode 13 | Monkey See, Monkey Duel | 2004-12-29 | 25 min |
| Season 1 | Episode 14 | A Spirit Summoned | 2005-01-05 | 25 min |
| Season 1 | Episode 15 | Courting Alexis | 2005-01-12 | 25 min |
| Season 1 | Episode 16 | The Duel Giant | 2005-01-19 | 25 min |
| Season 1 | Episode 17 | Nature of the Draw | 2005-01-26 | 25 min |
| Season 1 | Episode 18 | The King of Copycats (1) | 2005-02-02 | 25 min |
| Season 1 | Episode 19 | The King of Copycats (2) | 2005-02-09 | 25 min |
| Season 1 | Episode 20 | The Maiden in Love | 2005-02-16 | 25 min |
| Season 1 | Episode 21 | The Duel Off (1) | 2005-02-23 | 25 min |
| Season 1 | Episode 22 | The Duel Off (2) | 2005-03-02 | 25 min |
| Season 1 | Episode 23 | The Little Belowski | 2005-03-09 | 25 min |
| Season 1 | Episode 24 | The New Chazz | 2005-03-16 | 25 min |
| Season 1 | Episode 25 | The School Duel (1) | 2005-03-23 | 25 min |
| Season 1 | Episode 26 | The School Duel (2) | 2005-03-30 | 25 min |
| Season 1 | Episode 27 | Grave Risk (1) | 2005-04-06 | 25 min |
| Season 1 | Episode 28 | Grave Risk (2) | 2005-04-13 | 25 min |
| Season 1 | Episode 29 | Doomsday Day (1) | 2005-04-20 | 25 min |
| Season 1 | Episode 30 | Doomsday Day (2) | 2005-04-27 | 25 min |
| Season 1 | Episode 31 | Field of Screams (1) | 2005-05-04 | 25 min |
| Season 1 | Episode 32 | Field of Screams (2) | 2005-05-11 | 25 min |
| Season 1 | Episode 33 | Field of Screams (3) | 2005-05-18 | 25 min |
| Season 1 | Episode 34 | The Fear Factor | 2005-05-25 | 25 min |
| Season 1 | Episode 35 | Sibling Rivalry | 2005-06-01 | 25 min |
| Season 1 | Episode 36 | Duel Distractions (1) | 2005-06-08 | 25 min |
| Season 1 | Episode 37 | Duel Distractions (2) | 2005-06-13 | 25 min |
| Season 1 | Episode 38 | Get Yarr Game On! | 2005-06-22 | 25 min |
| Season 1 | Episode 39 | The Dark Scorpions | 2005-06-29 | 25 min |
| Season 1 | Episode 40 | A Lying Legend | 2005-07-06 | 25 min |
| Season 1 | Episode 41 | A Reason To Win | 2005-07-13 | 25 min |
| Season 1 | Episode 42 | Duel Monsters Spirit Day | 2005-07-20 | 25 min |
| Season 1 | Episode 43 | Hearts Are Wild | 2005-07-27 | 25 min |
| Season 1 | Episode 44 | The Seventh Shadow Rider | 2005-08-03 | 25 min |
| Season 1 | Episode 45 | Amnael's Endgame (1) | 2005-08-10 | 25 min |
| Season 1 | Episode 46 | Amnael's Endgame (2) | 2005-08-17 | 25 min |
| Season 1 | Episode 47 | Chazz-anova | 2005-08-24 | 25 min |
| Season 1 | Episode 48 | Rise of the Sacred Beasts (1) | 2005-08-31 | 25 min |
| Season 1 | Episode 49 | Rise of the Sacred Beasts (2) | 2005-09-07 | 25 min |
| Season 1 | Episode 50 | Magna Chum Laude | 2005-09-14 | 25 min |
| Season 1 | Episode 51 | The Graduation Match (1) | 2005-09-21 | 25 min |
| Season 1 | Episode 52 | The Graduation Match (2) | 2005-09-28 | 25 min |
| Season 2 | Episode 1 | Back to Duel | 2005-10-05 | 25 min |
| Season 2 | Episode 2 | Champion or Chazz-been | 2005-10-12 | 25 min |
| Season 2 | Episode 3 | A Hassleberry Hounding | 2005-10-19 | 25 min |
| Season 2 | Episode 4 | Sad But Truesdale | 2005-10-26 | 25 min |
| Season 2 | Episode 5 | The Demon | 2005-11-02 | 25 min |
| Season 2 | Episode 6 | A New Breed of Hero (1) | 2005-11-09 | 25 min |
| Season 2 | Episode 7 | A New Breed of Hero (2) | 2005-11-16 | 25 min |
| Season 2 | Episode 8 | Pop Goes the Duel | 2005-11-23 | 25 min |
| Season 2 | Episode 9 | I've Seen the Light | 2005-11-30 | 25 min |
| Season 2 | Episode 10 | A Greater Porpoise | 2005-12-07 | 25 min |
| Season 2 | Episode 11 | Curry Worries | 2005-12-14 | 25 min |
| Season 2 | Episode 12 | Camaraderie Contest | 2005-12-21 | 25 min |
| Season 2 | Episode 13 | No Pain, No Game | 2005-12-28 | 25 min |
| Season 2 | Episode 14 | Going Bananas | 2006-01-04 | 25 min |
| Season 2 | Episode 15 | Homecoming Duel (1) | 2006-01-11 | 25 min |
| Season 2 | Episode 16 | Homecoming Duel (2) | 2006-01-18 | 25 min |
| Season 2 | Episode 17 | Dormitory Demolition | 2006-01-25 | 25 min |
| Season 2 | Episode 18 | Obelisk White? | 2006-02-01 | 25 min |
| Season 2 | Episode 19 | DuelFellas | 2006-02-08 | 25 min |
| Season 2 | Episode 20 | Not Playing With A Full Deck | 2006-02-15 | 25 min |
| Season 2 | Episode 21 | Source of Strength | 2006-02-22 | 25 min |
| Season 2 | Episode 22 | Happily Never After | 2006-03-01 | 25 min |
| Season 2 | Episode 23 | Taken By Storm (1) | 2006-03-08 | 25 min |
| Season 2 | Episode 24 | Taken By Storm (2) | 2006-03-15 | 25 min |
| Season 2 | Episode 25 | J-Dawg and T-Bone | 2006-03-22 | 25 min |
| Season 2 | Episode 26 | Mirror, Mirror (1) | 2006-03-29 | 25 min |
| Season 2 | Episode 27 | Mirror, Mirror (2) | 2006-04-05 | 25 min |
| Season 2 | Episode 28 | What a Doll! | 2006-04-12 | 25 min |
| Season 2 | Episode 29 | Let's Make a Duel | 2006-04-19 | 25 min |
| Season 2 | Episode 30 | Magnetic Personality | 2006-04-26 | 25 min |
| Season 2 | Episode 31 | Schooling the Master | 2006-05-03 | 25 min |
| Season 2 | Episode 32 | Generation neXt | 2006-05-10 | 25 min |
| Season 2 | Episode 33 | Rah, Rah Ra! | 2006-05-17 | 25 min |
| Season 2 | Episode 34 | The Art of the Duel | 2006-05-24 | 25 min |
| Season 2 | Episode 35 | Blinded by the Light (1) | 2006-05-31 | 25 min |
| Season 2 | Episode 36 | Blinded by the Light (2) | 2006-06-07 | 25 min |
| Season 2 | Episode 37 | The Darkness Within | 2006-06-14 | 25 min |
| Season 2 | Episode 38 | Pro-Dueling | 2006-06-21 | 25 min |
| Season 2 | Episode 39 | Don't Fear the Reaper | 2006-06-28 | 25 min |
| Season 2 | Episode 40 | Duel for Hire | 2006-07-05 | 25 min |
| Season 2 | Episode 41 | Heart of Ice (1) | 2006-07-12 | 25 min |
| Season 2 | Episode 42 | Heart of Ice (2) | 2006-07-19 | 25 min |
| Season 2 | Episode 43 | Tough Love | 2006-07-26 | 25 min |
| Season 2 | Episode 44 | It's All Relative | 2006-08-02 | 25 min |
| Season 2 | Episode 45 | The Dark Light | 2006-08-09 | 25 min |
| Season 2 | Episode 46 | Ultimate Destiny | 2006-08-16 | 25 min |
| Season 2 | Episode 47 | The Key Factor | 2006-08-23 | 25 min |
| Season 2 | Episode 48 | The Phoenix Has Landed (1) | 2006-08-30 | 25 min |
| Season 2 | Episode 49 | The Phoenix Has Landed (2) | 2006-09-06 | 25 min |
| Season 2 | Episode 50 | The Hands of Justice (1) | 2006-09-13 | 25 min |
| Season 2 | Episode 51 | The Hands of Justice (2) | 2006-09-20 | 25 min |
| Season 2 | Episode 52 | Future Changes | 2006-09-27 | 25 min |
| Season 3 | Episode 1 | Third Time's a Charm | 2006-10-04 | 25 min |
| Season 3 | Episode 2 | Jewel of a Duel (1) | 2006-10-11 | 25 min |
| Season 3 | Episode 3 | Jewel of a Duel (2) | 2006-10-18 | 25 min |
| Season 3 | Episode 4 | Hanging with Axel (1) | 2006-11-01 | 25 min |
| Season 3 | Episode 5 | Hanging with Axel (2) | 2006-11-08 | 25 min |
| Season 3 | Episode 6 | Primal Instinct | 2006-11-15 | 25 min |
| Season 3 | Episode 7 | Head in the Clouds (1) | 2006-11-22 | 25 min |
| Season 3 | Episode 8 | Head in the Clouds (2) | 2006-11-29 | 25 min |
| Season 3 | Episode 9 | Win Mr. Stein's Duel (1) | 2006-12-06 | 25 min |
| Season 3 | Episode 10 | Win Mr. Stein's Duel (2) | 2006-12-13 | 25 min |
| Season 3 | Episode 11 | Trapper Keeper (1) | 2006-12-20 | 25 min |
| Season 3 | Episode 12 | Trapper Keeper (2) | 2006-12-27 | 25 min |
| Season 3 | Episode 13 | Snake in the Grass (1) | 2007-01-04 | 25 min |
| Season 3 | Episode 14 | Snake in the Grass (2) | 2006-01-10 | 25 min |
| Season 3 | Episode 15 | Snake in the Grass (3) | 2007-01-17 | 25 min |
| Season 3 | Episode 16 | Inter-Dimensional Detention | 2007-01-24 | 25 min |
| Season 3 | Episode 17 | Sub-Desert Duel | 2007-01-31 | 25 min |
| Season 3 | Episode 18 | Night of the Living Duelists | 2007-02-07 | 25 min |
| Season 3 | Episode 19 | School Ghoul Duels | 2007-02-14 | 25 min |
| Season 3 | Episode 20 | Triple Play (1) | 2007-02-21 | 25 min |
| Season 3 | Episode 21 | Triple Play (2) | 2007-02-28 | 25 min |
| Season 3 | Episode 22 | Return of the Sacred Beasts | 2007-03-07 | 25 min |
| Season 3 | Episode 23 | Breaking the Sacred Seal | 2007-03-14 | 25 min |
| Season 3 | Episode 24 | A Dimension Deal | 2007-03-21 | 25 min |
| Season 3 | Episode 25 | Unleash the Dragon (1) | 2007-03-28 | 25 min |
| Season 3 | Episode 26 | Unleash the Dragon (2) | 2007-04-04 | 25 min |
| Season 3 | Episode 27 | All for One | 2007-04-11 | 25 min |
| Season 3 | Episode 28 | A New World Order | 2007-04-18 | 25 min |
| Season 3 | Episode 29 | Friend or Fiend | 2007-04-25 | 25 min |
| Season 3 | Episode 30 | Dueling with a Dark Army | 2007-05-02 | 25 min |
| Season 3 | Episode 31 | Turning the Page (1) | 2007-05-09 | 25 min |
| Season 3 | Episode 32 | Turning the Page (2) | 2007-05-16 | 25 min |
| Season 3 | Episode 33 | The State of Syrus | 2007-05-23 | 25 min |
| Season 3 | Episode 34 | The Darkness Revealed | 2007-05-30 | 25 min |
| Season 3 | Episode 35 | A Sight Unseen (1) | 2007-06-06 | 25 min |
| Season 3 | Episode 36 | A Sight Unseen (2) | 2007-06-13 | 25 min |
| Season 3 | Episode 37 | What Lies Beneath (1) | 2007-06-20 | 25 min |
| Season 3 | Episode 38 | What Lies Beneath (2) | 2007-06-27 | 25 min |
| Season 3 | Episode 39 | What Lies Beneath (3) | 2007-07-04 | 25 min |
| Season 3 | Episode 40 | The Forbidden Ritual (1) | 2007-07-11 | 25 min |
| Season 3 | Episode 41 | The Forbidden Ritual (2) | 2007-07-18 | 25 min |
| Season 3 | Episode 42 | Conquering the Past (1) | 2007-07-25 | 25 min |
| Season 3 | Episode 43 | Conquering the Past (2) | 2007-08-08 | 25 min |
| Season 3 | Episode 44 | Conquering the Past (3) | 2007-08-15 | 25 min |
| Season 3 | Episode 45 | The Ultimate Face-Off (1) | 2007-08-22 | 25 min |
| Season 3 | Episode 46 | The Ultimate Face-Off (2) | 2007-08-29 | 25 min |
| Season 3 | Episode 47 | The Power Within (1) | 2007-09-05 | 25 min |
| Season 3 | Episode 48 | The Power Within (2) | 2007-09-12 | 25 min |
| Season 3 | Episode 49 | Return of the Supreme King (1) | 2007-09-19 | 25 min |
| Season 3 | Episode 50 | Return of the Supreme King (2) | 2007-09-26 | 25 min |
| Season 3 | Episode 51 | Return of the Supreme King (3) | 2007-10-03 | 25 min |
| Season 3 | Episode 52 | Judai Revived!? A Brand NEW Journey! | 2007-10-10 | 25 min |
| Season 4 | Episode 1 | A Looming Threat! The Mysterious Visitor | 2007-10-17 | 25 min |
| Season 4 | Episode 2 | Farewell, Duel Academia! The Path Judai Chooses! | 2007-10-24 | 25 min |
| Season 4 | Episode 3 | The Truth Behind Darkness! Judai vs. Fubuki | 2007-10-31 | 25 min |
| Season 4 | Episode 4 | Fusing Souls! Neos vs. Five God Dragon | 2007-11-07 | 25 min |
| Season 4 | Episode 5 | Shall we Duel? Invitation to a Pair Duel | 2007-11-14 | 25 min |
| Season 4 | Episode 6 | Judai vs. Asuka! Face-Down Card of Hidden Emotions | 2007-11-21 | 25 min |
| Season 4 | Episode 7 | Challenge from Psycho Shocker | 2007-11-28 | 25 min |
| Season 4 | Episode 8 | The Inherited Cyber-Dark Dragon | 2007-12-05 | 25 min |
| Season 4 | Episode 9 | Shoot For It! Manjyome, the Path to a Pro Duelist! | 2007-12-12 | 25 min |
| Season 4 | Episode 10 | Armed Dragon vs. Dragoon D End | 2007-12-19 | 25 min |
| Season 4 | Episode 11 | Graduation Duel! Chronos vs. the Original Dropout Boy | 2007-12-26 | 25 min |
| Season 4 | Episode 12 | Graduation Duel Starts! Neos vs. Horus the Black Flame Dragon | 2008-01-04 | 25 min |
| Season 4 | Episode 13 | The Price of Decision! O'Brien, Darkness in Fire | 2008-01-09 | 25 min |
| Season 4 | Episode 14 | Saiou Returns! Activate! | 2008-01-16 | 25 min |
| Season 4 | Episode 15 | The End of Destiny! Magma Neos vs. The Dark Ruler | 2008-01-23 | 25 min |
| Season 4 | Episode 16 | Duel Academia Crisis! The Jewel Beasts Blocking the Way! | 2008-01-30 | 25 min |
| Season 4 | Episode 17 | Darkness Invasion, The Stolen Memories | 2008-02-06 | 25 min |
| Season 4 | Episode 18 | Activate, Clear World! Ferocious Negative Effect | 2008-02-13 | 25 min |
| Season 4 | Episode 19 | Battle Royale! Judai vs. Johan vs. Fujiwara | 2008-02-20 | 25 min |
| Season 4 | Episode 20 | Rainbown Neos, Protector of Bonds vs. Clear Vicious Knight | 2008-02-27 | 25 min |
| Season 4 | Episode 21 | The Combo of Terror, Nihilty and Infinity | 2008-03-05 | 25 min |
| Season 4 | Episode 22 | Final Hope! Yuki Judai | 2008-03-12 | 25 min |
| Season 4 | Episode 23 | Goodbye Judai! Tears of Graduation | 2008-03-19 | 25 min |
| Season 4 | Episode 24 | The True Graduation Duel! Judai vs. Legendary Duelist | 2008-03-26 | 25 min |
| Directing | Hatsuki Tsuji | Series Director |
| Visual Effects | Ayami Minowa | Color Designer |
| Art | Junichiro Nishikawa | Art Direction |
| Sound | Takuya Hiramitsu | Sound Director |
| Sound | Yutaka Minobe | Original Music Composer |
| Sound | YOFFY | Theme Song Performance |
| Sound | IMAJO | Theme Song Performance |
| Visual Effects | Kenichi Hara | Character Designer |
