| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Things Change | 1 | 1 | Saturday February 8, 2003 |
| A Better Mousetrap (1) | 1 | 2 | Saturday February 15, 2003 |
| Attack of the Mousers (2) | 1 | 3 | Saturday February 22, 2003 |
| Meet Casey Jones | 1 | 4 | Saturday March 1, 2003 |
| Nano | 1 | 5 | Saturday March 8, 2003 |
| Darkness on the Edge of Town | 1 | 6 | Saturday March 15, 2003 |
| The Way of Invisibility | 1 | 7 | Saturday March 22, 2003 |
| Fallen Angel | 1 | 8 | Saturday March 29, 2003 |
| Garbageman | 1 | 9 | Saturday April 5, 2003 |
| The Shredder Strikes (1) | 1 | 10 | Saturday April 12, 2003 |
| The Shredder Strikes (2) | 1 | 11 | Saturday April 19, 2003 |
| The Unconvincing Turtle Titan | 1 | 12 | Saturday May 3, 2003 |
| Notes from the Underground (1) | 1 | 13 | Saturday May 10, 2003 |
| Notes from the Underground (2) | 1 | 14 | Saturday May 17, 2003 |
| Notes from the Underground (3) | 1 | 15 | Saturday May 24, 2003 |
| The King | 1 | 16 | Saturday May 31, 2003 |
| The Shredder Strikes Back (1) | 1 | 17 | Saturday June 7, 2003 |
| The Shredder Strikes Back (2) | 1 | 18 | Saturday June 14, 2003 |
| Tales of Leo | 1 | 19 | Saturday September 13, 2003 |
| The Monster Hunter | 1 | 20 | Saturday September 20, 2003 |
| Return to New York (1) | 1 | 21 | Saturday September 27, 2003 |
| Return to New York (2) | 1 | 22 | Saturday October 4, 2003 |
| Return to New York (3) | 1 | 23 | Saturday October 11, 2003 |
| Lone Raph and Cub | 1 | 24 | Saturday October 18, 2003 |
| The Search for Splinter (1) | 1 | 25 | Saturday October 25, 2003 |
| The Search for Splinter (2) | 1 | 26 | Saturday November 1, 2003 |