| Title | Season | Episode # | First Aired |
|---|---|---|---|
| No Pain, No Game | 2 | 65 | Thursday September 7, 2006 |
| Not Playing With A Full Deck | 2 | 72 | Tuesday October 10, 2006 |
| Obelisk White? | 2 | 70 | Thursday October 5, 2006 |
| Pop Goes the Duel | 2 | 60 | Wednesday August 30, 2006 |
| Primal Instinct | 3 | 110 | Saturday May 26, 2007 |
| Pro-Dueling | 2 | 90 | Thursday February 1, 2007 |
| Rah, Rah Ra! | 2 | 85 | Saturday December 23, 2006 |
| Rainbow Neos! Protector of Bonds VS Clear Vicious Knight! | 4 | 176 | |
| Return of the Sacred Beasts | 3 | 126 | Saturday November 10, 2007 |
| Rise of the Sacred Beasts (1) | 1 | 48 | Friday March 31, 2006 |
| Rise of the Sacred Beasts (2) | 1 | 49 | Monday April 3, 2006 |
| Sad But Truesdale | 2 | 56 | Thursday August 24, 2006 |
| Saiou Returns! Activate the Decisive Power of Absolute Destiny! | 4 | 170 | |
| School Duel (1) | 1 | 25 | Monday December 12, 2005 |
| School Duel (2) | 1 | 26 | Tuesday December 13, 2005 |
| School Ghoul Duels | 3 | 123 | Saturday October 13, 2007 |
| Schooling the Master | 2 | 83 | Saturday December 9, 2006 |
| Shall We Duel? Invitation to a Pair Duel! | 4 | 161 | |
| Shoot for it! Chazz, the Path to a Pro Duelist! | 4 | 165 | |
| Sibling Rivalry | 1 | 35 | Tuesday February 7, 2006 |
| Source of Strength | 2 | 73 | Wednesday October 11, 2006 |
| Sub-Desert Duel | 3 | 121 | Saturday September 29, 2007 |
| Summon Yubel! | 3 | 150 | |
| Supreme King Jaden Resurrected! | 3 | 154 |
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