| Title | Season | Episode # | First Aired |
|---|---|---|---|
| 20,000 Leaks Under the City | 3 | 9 | Thursday October 5, 1989 |
| A Real Snow Job | 7 | 3 | Saturday September 25, 1993 |
| A Thing About Rats | 1 | 3 | Wednesday December 30, 1987 |
| A Turtle in Time (2) | 10 | 4 | Saturday October 5, 1996 |
| Adventures in Turtle-Sitting | 6 | 11 | Saturday October 24, 1992 |
| April Gets in Dutch | 7 | 11 | Saturday October 23, 1993 |
| April's Fool [A.K.A. April Foolish] | 3 | 35 | Friday December 1, 1989 |
| Artless | 7 | 5 | Saturday October 2, 1993 |
| Atlantis Awakes | 7 | 23 | Saturday December 4, 1993 |
| Attack of Big MACC | 3 | 14 | Thursday October 12, 1989 |
| Attack of the 50 Foot Irma | 3 | 4 | Thursday September 28, 1989 |
| Attack of the Neutrinos | 7 | 20 | Saturday November 20, 1993 |
| Back to the Egg | 4 | 13 | Wednesday September 26, 1990 |
| Bebop and Rocksteady Conquer the Universe | 4 | 20 | Saturday September 22, 1990 |
| Beneath These Streets | 3 | 1 | Monday September 25, 1989 |
| Beware the Lotus | 3 | 18 | Wednesday November 1, 1989 |
| Beyond the Donatello Nebula | 4 | 38 | Saturday December 1, 1990 |
| Blast from the Past | 3 | 20 | Friday November 3, 1989 |
| Burne's Blues | 3 | 10 | Friday October 6, 1989 |
| Bye, Bye, Fly | 3 | 32 | Friday November 24, 1989 |
| Camera Bugged | 3 | 15 | Friday October 13, 1989 |
| Carter, the Enforcer | 9 | 7 | Saturday October 28, 1995 |
| Case of the Hot Kimono | 3 | 30 | Monday November 20, 1989 |
| Casey Jones: Outlaw Hero | 3 | 21 | Tuesday November 7, 1989 |
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