Season 1
1. Turtle Tracks
2. Enter the Shredder
3. Thing About Rats
4. Hot Rodding Teenagers from Dimension X
5. Shredder & Splintered

Season 2
1. Return of the Shredder
2. The Incredible Shrinking Turtles
3. It Came from Beneath the Sewers
4. The Mean Machines
5. Curse of the Evil Eye
6. Case of the Killer Pizzas
7. Enter: the Fly
8. Invasion of the Punk Frogs
9. New York's Shiniest
10. Splinter No More
11. Teenagers from Dimension X
12. The Catwoman from Channel Six
13. Return of the Technodrome

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

Season 4
1. Plan Six from Outer Space
2. Turtles of the Jungle
3. Michaelangelo Toys Around
4. Peking Turtle
5. Shredder's Mom
6. Four Turtles and a Baby
7. Turtlemaniac
8. Rondo in New York
9. Planet of the Turtles
10. Name That Toon
11. Menace, Maestro, Please
12. Superhero for a Day
13. Back to the Egg
14. Son of the Return of the Fly II
15. Raphael Knocks 'Em Dead
16. Bebop and Rocksteady Conquer the Universe
17. Raphael Meets His Match
18. Slash, the Evil Turtle from Dimension X
19. Leonardo Lightens Up
20. Were-Rats from Channel 6
21. Funny, They Shrunk Michaelangelo
22. The Big Zipp Attack
23. Donatello Makes Time
24. Farewell, Lotus Blossom
25. Rebel Without a Fin
26. Poor Little Rich Turtle
27. What's Michaelangelo Good For?
28. The Dimension X Story
29. Donatello's Degree
30. The Big Cufflink Caper!
31. Raphael Drives 'Em Wild
32. Beyond the Donatello Nebula
33. The Big Bug Blunder
34. The Foot Soldiers Are Revolting
35. Unidentified Flying Leonardo
36. The Adventures of Rhino-Man
37. Michaelangelo Meets Bugman
38. Leonardo Versus Tempestra
39. Splinter Vanishes

Season 5
1. The Turtles and the Hare
2. Once Upon a Time Machine
3. My Brother, the Bad Guy
4. Michaelangelo Meets Mondo Gecko
5. Enter Mutagen Man
6. Donatello's Badd Time
7. Michaelangelo Meets Bugman Again
8. Muckman Messes Up
9. Napoleon Bonafrog: Colossus of the Swamps
10. Raphael vs. the Volcano
11. Landlord of the Flies
12. Donatello's Duplicate
13. The Ice Creature Cometh
14. Leonardo Cuts Loose
15. Pirate Radio
16. Turtle of a Thousand Faces
17. Leonardo, the Renaissance Turtle
18. Zach and the Alien Invaders
19. Welcome Back, Polarisoids
20. Michelangelo, the Sacred Turtle
21. Planet of the Turtleoids Part 1
22. Planet of the Turtleoids Part 2

Season 6
1. Rock Around the Block
2. Krangenstein Lives
3. Super Irma
4. Adventures in Turtle Sitting
5. The Sword of Yurikawa
7. Shreeka's Revenge
8. Too Hot to Handle
9. Nightmare in the Lair
10. Phantom of the Sewers
11. Donatello Trashes Slash
12. Leonardo Is Missing
13. Snakes Alive!
14. Polly Wanna Pizza
15. Mr. Nice Guy
16. Sleuth on the Loose

Season 7
1a. Tower of Power
1b. Tower of Power
2. Rust Never Sleeps
3. A Real Snow Job
4. Venice on the Half Shell
5. Artless
6. Ring of Fire
7. The Irish Jig Is Up
8. Shredder's New Sword
9. The Lost Queen of Atlantis
10. Turtles on the Orient Express
11. April Gets in Dutch
12. Northern Lights Out
13. Elementary, My Dear Tortoise
14. Night of the Dark Turtle
15. The Starchild
16. The Legend of Koji
17. Convicts from Dimension X
18. White Belt, Black Heart
19. Night of the Rogues
20. Attack of the Neutrinos
21. Escape from the Planet of the Turtleoids
22. Revenge of the Fly
23. Atlantis Awakes
24. Dirk Savage: Mutant Hunter
25. Invasion of the Krangazoids
26. Combat Land
27. Shredder Triumphant

Season 8
1. Get Shredder!
2. Wrath of the Rat King
3. State of Shock
4. Cry HAVOC!
5. HAVOC in the Streets
6. Enter: Krakus
7. Cyber Turtles
8. Turtle Trek

Season 9
1. The Unknown Ninja
2. Dregg of the Earth
3. The Wrath of Medusa
4. The New Mutation
5. The Showdown
6. Split-Second
7. Carter, the Enforcer
8. Doomquest

Season 10
1. The Return of Dregg
2. The Beginning of the End
3. The Power of Three Part 1
4. A Turtle in Time Part 2
5. Turtles to the Second Power Part 3
6. Mobster from Dimension X
7. The Day the Earth Disappeared
8. Divide and Conquer