| Title | Season | Episode # | First Aired |
|---|---|---|---|
| The Resurrection Monster | 1 | 20 | Friday March 15, 2002 |
| The Road to the Republic | 1 | 8 | Wednesday February 27, 2002 |
| The Saviour | 1 | 27 | Tuesday March 26, 2002 |
| The Secret Mission | 2 | 35 | Friday April 5, 2002 |
| The Sensational Three: Rematch with Jack Cisco | 3 | 78 | Tuesday November 6, 2001 |
| The Shadow Fox: Brad's Betrayal | 3 | 87 | Tuesday November 20, 2001 |
| The Steel Bison | 2 | 38 | Wednesday April 10, 2002 |
| The Third Conversion: Zero Panzer's Debut! | 3 | 86 | Monday November 19, 2001 |
| The Three Guards | 1 | 31 | Monday April 1, 2002 |
| The Unseen Enemy (1) | 4 | 100 | Saturday November 15, 2003 |
| The Valley of the Monster | 1 | 9 | Thursday February 28, 2002 |
| The Waters Surface and the Undercurrent | 4 | 114 | |
| The Wings of Darkness | 2 | 45 | Friday April 19, 2002 |
| The Zoid Hunters | 2 | 40 | Friday April 12, 2002 |
| Three Teams Face Off (2) | 4 | 106 | Saturday December 27, 2003 |
| Tournament of Heroes: The Royal Cup (1) | 3 | 91 | Tuesday November 27, 2001 |
| Triumphant Castle Enterance | 5 | 158 | |
| Underground Water Passage | 5 | 127 | |
| Unsanctioned Battle: The Mysterious Backdraft Group | 3 | 71 | Friday October 26, 2001 |
| Van's New Power | 2 | 52 | Tuesday April 30, 2002 |
| Visitor from the Past | 4 | 103 | Saturday December 6, 2003 |
| Wake Up! Zeek! | 1 | 14 | Thursday March 7, 2002 |
| Warriors On Vacation: The Storm Sworders | 3 | 84 | Wednesday November 14, 2001 |
| Zero Is Stolen: The Fiery Battle (1) | 3 | 79 | Wednesday November 7, 2001 |
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