| Title | Season | Episode # | First Aired |
|---|---|---|---|
| The King of the Copycats (1) | 1 | 18 | Thursday November 17, 2005 |
| The King of the Copycats (2) | 1 | 19 | Friday November 18, 2005 |
| The Last Hope! Jaden Yuki! | 4 | 178 | |
| The Little Belowski | 1 | 23 | Thursday December 8, 2005 |
| The Maiden In Love | 1 | 20 | Monday November 21, 2005 |
| The New Chazz | 1 | 24 | Friday December 9, 2005 |
| The Next King of Games | 1 | 1 | Monday October 10, 2005 |
| The Phoenix Has Landed (1) | 2 | 100 | Friday February 16, 2007 |
| The Phoenix Has Landed (2) | 2 | 101 | Tuesday February 20, 2007 |
| The Price of Decision! Axel, Darkness in the Fire! | 4 | 169 | |
| The Sealed Fusion | 3 | 146 | |
| The Seventh Shadow Rider | 1 | 44 | Monday March 27, 2006 |
| The Shadow Duelist (1) | 1 | 5 | Monday October 17, 2005 |
| The Shadow Duelist (2) | 1 | 6 | Tuesday October 18, 2005 |
| The State of Syrus | 3 | 137 | Saturday March 29, 2008 |
| The True Graduation Duel! Jaden VS The Legendary Duelist! | 4 | 180 | |
| The Truth Behind Nightshroud! Jaden vs. Atticus! | 4 | 159 | |
| The Ultimate Dragon Showdown! Cyber End VS Rainbow Dark | 3 | 148 | |
| Third Time's A Charm | 3 | 105 | Saturday April 7, 2007 |
| Tough Love | 2 | 95 | Friday February 9, 2007 |
| Trapper Keeper (1) | 3 | 115 | Saturday July 28, 2007 |
| Trapper Keeper (2) | 3 | 116 | Saturday August 4, 2007 |
| Triple Play (1) | 3 | 124 | Saturday October 20, 2007 |
| Triple Play (2) | 3 | 125 | Saturday November 3, 2007 |
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