Season 1 (5 episodes)
- 1. Episode 1 Turtle Tracks
- 2. Episode 2 Enter the Shredder
- 3. Episode 3 A Thing About Rats
- 4. Episode 4 Hot Rodding Teenagers from Dimension X
- 5. Episode 5 Shredded & Splintered
Season 2 (13 episodes)
- 1. Episode 1 Return of the Shredder
- 2. Episode 2 The Incredible Shrinking Turtles
- 3. Episode 3 It Came from Beneath the Sewers
- 4. Episode 4 The Mean Machines
- 5. Episode 5 Curse of the Evil Eye
- 6. Episode 6
- 7. Episode 7
- 8. Episode 8
- 9. Episode 9
- 10. Episode 10
- 11. Episode 11
- 12. Episode 12
- 13. Episode 13
Season 3 (44 episodes)
- 1. Episode 1
- 2. Episode 2
- 3. Episode 3
- 4. Episode 4
- 5. Episode 5
- 6. Episode 6
- 7. Episode 7
- 8. Episode 8
- 9. Episode 9
- 10. Episode 10
- 11. Episode 11
- 12. Episode 12
- 13. Episode 13
- 14. Episode 14
- 15. Episode 15
- 16. Episode 16
- 17. Episode 17
- 18. Episode 18
- 19. Episode 19
- 20. Episode 20
- 21. Episode 21
- 22. Episode 22
- 23. Episode 23
- 24. Episode 24
- 25. Episode 25
- 26. Episode 26
- 27. Episode 27
- 28. Episode 28
- 29. Episode 29
- 30. Episode 30
- 31. Episode 31
- 32. Episode 32
- 33. Episode 33
- 34. Episode 34
- 35. Episode 35
- 36. Episode 36
- 37. Episode 37
- 38. Episode 38
- 39. Episode 39
- 40. Episode 40
- 41. Episode 41
- 42. Episode 42
- 43. Episode 43
- 44. Episode 44
Season 4 (40 episodes)
- 1. Episode 1 Plan Six from Outer Space
- 2. Episode 2 Turtles of the Jungle
- 3. Episode 3 Michaelangelo Toys Around
- 4. Episode 4 Peking Turtle
- 5. Episode 5 Shredders Mom
- 6. Episode 6 Four Turtles and a Baby
- 7. Episode 7 Turtlemaniac
- 8. Episode 8 Rondo in New York
- 9. Episode 9 Planet of the Turtles
- 10. Episode 10 Name That Toon
- 11. Episode 11 Menace Maestro, Please
- 12. Episode 12 Superhero for a Day
- 13. Episode 13 Back to the Egg
- 14. Episode 14 The Turtles and the Hare (1)
- 15. Episode 15 Once Upon a Time Machine (2)
- 16. Episode 16 The Dimension X Story
- 17. Episode 17 Donatellos Degree
- 18. Episode 18 Son of Return of the Fly II
- 19. Episode 19 Raphael Knocks Em Dead
- 20. Episode 20 Bebop and Rocksteady Conquer the Universe
- 21. Episode 21 Raphael Meets His Match
- 22. Episode 22 Slash - The Evil Turtle from Dimension X
- 23. Episode 23 Leonardo Lightens Up
- 24. Episode 24 Were-Rats from Channel 6
- 25. Episode 25 Funny, They Shrunk Michaelangelo
- 26. Episode 26 The Big Zipp Attack
- 27. Episode 27 Donatello Makes Time
- 28. Episode 28 Farewell, Lotus Blossom
- 29. Episode 29 Rebel Without a Fin
- 30. Episode 30 The Adventures of Rhino-Man (A.K.A .Rhino-Man)
- 31. Episode 31 Michaelangelo Meets Bugman
- 32. Episode 32 Poor Little Rich Turtle
- 33. Episode 33 Whats Michaelangelo Good For?
- 34. Episode 34 The Big Cufflink Caper!
- 35. Episode 35 Leonardo Versus Tempestra
- 36. Episode 36 Splinter Vanishes
- 37. Episode 37 Raphael Drives Em Wild
- 38. Episode 38 Beyond the Donatello Nebula
- 39. Episode 39 The Big Bug Blunder
- 40. Episode 40 The Foot Soldiers are Revolting
Season 5 (18 episodes)
- 1. Episode 1 Planet of the Turtleoids (1)
- 2. Episode 2 Planet of the Turtleoids (2)
- 3. Episode 3 My Brother, the Bad Guy
- 4. Episode 4 Michaelangelo Meets Mondo Gecko
- 5. Episode 5 Enter: Mutagen Man
- 6. Episode 6 Donatellos Badd Time
- 7. Episode 7 Michaelangelo Meets Bugman Again
- 8. Episode 8 Muckman Messes Up
- 9. Episode 9 Napoleon Bonafrog: Colossus of the Swamps
- 10. Episode 10 Raphael Versus the Volcano
- 11. Episode 11 Landlord of the Flies
- 12. Episode 12 Donatellos Duplicate
- 13. Episode 13 The Ice Creature Cometh
- 14. Episode 14 Leonardo Cuts Loose
- 15. Episode 15 Pirate Radio
- 16. Episode 16 Raphael, Turtle of a Thousand Faces
- 17. Episode 17 Leonardo, The Renaissance Turtle
- 18. Episode 18 Zach and the Alien Invaders
Season 6 (16 episodes)
- 1. Episode 1 Rock Around the Block
- 2. Episode 2 Leonardo is Missing
- 3. Episode 3 Krangenstein Lives!
- 4. Episode 4 Return of the Turtleoid
- 5. Episode 5 Super Irma
- 6. Episode 6 Too Hot to Handle
- 7. Episode 7 Shreekas Revenge
- 8. Episode 8 Donatello Trashes Slash
- 9. Episode 9 Sword of Yurikawa
- 10. Episode 10 Nightmare in the Lair
- 11. Episode 11 Adventures in Turtle-Sitting
- 12. Episode 12 Phantom of the Sewers
- 13. Episode 13 Snakes Alive!
- 14. Episode 14 Polly Wanna Pizza
- 15. Episode 15 Mr. Nice Guy
- 16. Episode 16 Sleuth on the Loose
Season 7 (27 episodes)
- 1. Episode 1 Tower of Power
- 2. Episode 2 Rust Never Sleeps
- 3. Episode 3 A Real Snow Job
- 4. Episode 4 Venice on the Half Shell
- 5. Episode 5 Artless
- 6. Episode 6 Ring of Fire
- 7. Episode 7 The Irish Jig is Up
- 8. Episode 8 Shredders New Sword
- 9. Episode 9 The Lost Queen of Atlantis
- 10. Episode 10 Turtles on the Orient Express
- 11. Episode 11 April Gets in Dutch
- 12. Episode 12 Northern Lights Out
- 13. Episode 13 Elementary, My Dear Turtle
- 14. Episode 14 Night of the Dark Turtle
- 15. Episode 15 The Starchild
- 16. Episode 16 The Legend of Koji
- 17. Episode 17 Convicts from Dimension X
- 18. Episode 18 White Belt, Black Heart
- 19. Episode 19 Night of the Rogues
- 20. Episode 20 Attack of the Neutrinos
- 21. Episode 21 Escape from the Planet of the Turtleloids
- 22. Episode 22 Revenge of the Fly
- 23. Episode 23 Atlantis Awakes
- 24. Episode 24 Dirk Savage: Mutant Hunter!
- 25. Episode 25 Invasion of the Krangazoids
- 26. Episode 26 Combat Land
- 27. Episode 27 Shredder Triumphant!
Season 8 (8 episodes)
- 1. Episode 1 Get Shredder!
- 2. Episode 2 Wrath of the Rat King
- 3. Episode 3 State of Shock
- 4. Episode 4 Cry H.A.V.O.C.! (1)
- 5. Episode 5 H.A.V.O.C. in the Streets (2)
- 6. Episode 6 Enter: Krakus (3)
- 7. Episode 7 Cyber-Turtles
- 8. Episode 8 Turtle Trek
Season 9 (8 episodes)
- 1. Episode 1 The Unknown Ninja
- 2. Episode 2 Dregg of the Earth
- 3. Episode 3 The Wrath of Medusa
- 4. Episode 4 The New Mutation
- 5. Episode 5 The Showdown
- 6. Episode 6 Split-Second
- 7. Episode 7 Carter, the Enforcer
- 8. Episode 8 Doomquest