| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Back to Duel | 2 | 53 | Monday August 21, 2006 |
| Battle Royal! Jaden VS Jesse VS Fujiwara! | 4 | 175 | |
| Blinded by the Light (1) | 2 | 87 | Saturday January 13, 2007 |
| Blinded by the Light (2) | 2 | 88 | Saturday January 20, 2007 |
| Breaking of the Sacred Seal! | 3 | 127 | Saturday January 19, 2008 |
| Camaraderie Contest | 2 | 64 | Wednesday September 6, 2006 |
| Challenge from Psycho Shocker | 4 | 163 | |
| Champion or Chazz-been | 2 | 54 | Tuesday August 22, 2006 |
| Chazz-anova | 1 | 47 | Thursday March 30, 2006 |
| Clash of the Demon Gods! Mythic Demon VS Exodia! | 3 | 149 | |
| Confrontation of the Chosen Cards! Elemental Heroes VS Yubel! | 3 | 153 | |
| Courting Alexis | 1 | 15 | Monday November 14, 2005 |
| Curry Worries | 2 | 63 | Tuesday September 5, 2006 |
| Darkness Invasion! Stolen Memories! | 4 | 173 | |
| Don't Fear the Reaper | 2 | 91 | Monday February 5, 2007 |
| Doomsday Duel (1) | 1 | 29 | Monday January 30, 2006 |
| Doomsday Duel (2) | 1 | 30 | Tuesday January 31, 2006 |
| Dormitory Demolition | 2 | 69 | Wednesday October 4, 2006 |
| Duel Academy Crisis! The Crystal Beasts Blocking the Way! | 4 | 172 | |
| Duel and Unusual Punishment | 1 | 7 | Wednesday October 19, 2005 |
| Duel Distractions (1) | 1 | 36 | Wednesday February 8, 2006 |
| Duel Distractions (2) | 1 | 37 | Thursday February 9, 2006 |
| Duel for Hire | 2 | 92 | Tuesday February 6, 2007 |
| Duel Monsters Spirit Day | 1 | 42 | Thursday March 2, 2006 |
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