| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Beneath These Streets | 3 | 1 | Monday September 25, 1989 |
| Sky Turtles | 3 | 2 | Tuesday September 26, 1989 |
| Turtles on Trial | 3 | 3 | Wednesday September 27, 1989 |
| Attack of the 50 Foot Irma | 3 | 4 | Thursday September 28, 1989 |
| The Maltese Hamster | 3 | 5 | Friday September 29, 1989 |
| Cowabunga Shredhead | 3 | 6 | Monday October 2, 1989 |
| The Fifth Turtle | 3 | 7 | Tuesday October 3, 1989 |
| The Ninja Sword of Nowhere | 3 | 8 | Wednesday October 4, 1989 |
| 20,000 Leaks Under the City | 3 | 9 | Thursday October 5, 1989 |
| Burne's Blues | 3 | 10 | Friday October 6, 1989 |
| Super Bebop and Mighty Rocksteady | 3 | 11 | Monday October 9, 1989 |
| Enter the Rat King | 3 | 12 | Tuesday October 10, 1989 |
| The Old Switcheroo | 3 | 13 | Wednesday October 11, 1989 |
| Attack of Big MACC | 3 | 14 | Thursday October 12, 1989 |
| Camera Bugged | 3 | 15 | Friday October 13, 1989 |
| Four Musketurtles | 3 | 16 | Monday October 30, 1989 |
| Turtles At the Earth's Core | 3 | 17 | Tuesday October 31, 1989 |
| Beware the Lotus | 3 | 18 | Wednesday November 1, 1989 |
| Take Me to Your Leader | 3 | 19 | Thursday November 2, 1989 |
| Blast from the Past | 3 | 20 | Friday November 3, 1989 |
| Casey Jones: Outlaw Hero | 3 | 21 | Tuesday November 7, 1989 |
| Turtles, Turtles Everywhere | 3 | 22 | Wednesday November 8, 1989 |
| Leatherhead: Terror of the Swamp | 3 | 23 | Thursday November 9, 1989 |
| Corporate Raiders from Dimension X | 3 | 24 | Friday November 10, 1989 |
| Usagi Yojimbo | 3 | 25 | Monday November 13, 1989 |
| Invasion of the Turtle Snatchers | 3 | 26 | Tuesday November 14, 1989 |
| Mutagen Monster | 3 | 27 | Wednesday November 15, 1989 |
| Shredderville | 3 | 28 | Wednesday November 15, 1989 |
| The Turtle Terminator | 3 | 29 | Friday November 17, 1989 |
| Case of the Hot Kimono | 3 | 30 | Monday November 20, 1989 |
| Return of the Fly | 3 | 31 | Wednesday November 22, 1989 |
| Bye, Bye, Fly | 3 | 32 | Friday November 24, 1989 |
| The Making of Metalhead | 3 | 33 | Monday November 27, 1989 |
| Leatherhead Meets the Rat King | 3 | 34 | Wednesday November 29, 1989 |
| April's Fool [A.K.A. April Foolish] | 3 | 35 | Friday December 1, 1989 |
| Green with Jealousy | 3 | 36 | Monday December 4, 1989 |
| Usagi Come Home | 3 | 37 | Tuesday December 5, 1989 |
| Mister Ogg Goes to Town | 3 | 38 | Thursday December 7, 1989 |
| The Great Boldini | 3 | 39 | Friday December 8, 1989 |
| Michaelangelo's Birthday | 3 | 40 | Friday February 2, 1990 |
| Pizza By the Shred | 3 | 41 | Tuesday February 6, 1990 |
| The Big Rip-Off (1) | 3 | 42 | Wednesday February 7, 1990 |
| The Big Break-In (2) | 3 | 43 | Thursday February 8, 1990 |
| The Big Blow Out (3) | 3 | 44 | Friday February 9, 1990 |
| The Grybyx | 3 | 45 | Monday May 14, 1990 |
| The Gang's All Here | 3 | 46 | Wednesday May 16, 1990 |
| The Missing Map | 3 | 47 | Tuesday July 24, 1990 |