Season 1 (23 episodes)
- 1. Episode 1 Things Change
- 2. Episode 2 A Better Mousetrap (1)
- 3. Episode 3 Attack of the Mousers (2)
- 4. Episode 4 Meet Casey Jones
- 5. Episode 5 Nano
- 6. Episode 6 Darkness on the Edge of Town
- 7. Episode 7 The Way of Invisibility
- 8. Episode 8 Fallen Angel
- 9. Episode 9 Garbageman
- 10. Episode 10 The Shredder Strikes (1)
- 11. Episode 11 The Shredder Strikes (2)
- 12. Episode 12 The Unconvincing Turtle Titan
- 13. Episode 13 Notes from the Underground (1)
- 14. Episode 14 Notes from the Underground (2)
- 15. Episode 15 Notes from the Underground (3)
- 16. Episode 16 The King
- 17. Episode 17 The Shredder Strikes Back (1)
- 18. Episode 18 The Shredder Strikes Back (2)
- 19. Episode 19 Tales of Leo
- 20. Episode 20 The Monster Hunter
- 21. Episode 21 Return to New York (1)
- 22. Episode 22 Return to New York (2)
- 23. Episode 23 Return to New York (3)
Season 2 (26 episodes)
- 1. Episode 1 Turtles in Space (1): The Fugitoid
- 2. Episode 2 Turtles in Space (2): The Trouble with Triceratons
- 3. Episode 3 Turtles in Space (3): The Big House
- 4. Episode 4 Turtles in Space (4): The Arena
- 5. Episode 5 Turtles in Space (5): Triceraton Wars
- 6. Episode 6 Secret Origins (1)
- 7. Episode 7 Secret Origins (2)
- 8. Episode 8 Secret Origins (3)
- 9. Episode 9 The Ultimate Ninja
- 10. Episode 10 Reflections
- 11. Episode 11 Modern Love - The Return of Nano
- 12. Episode 12 What a Croc
- 13. Episode 13 Return to the Underground
- 14. Episode 14 City at War (1)
- 15. Episode 15 City at War (2)
- 16. Episode 16 City at War (3)
- 17. Episode 17 Junklantis
- 18. Episode 18 The Golden Puck
- 19. Episode 19 Rogue in the House (1)
- 20. Episode 20 Rogue in the House (2)
- 21. Episode 21 Aprils Artifact
- 22. Episode 22 Return of the Justice Force
- 23. Episode 23 The Big Brawl (1)
- 24. Episode 24 The Big Brawl (2)
- 25. Episode 25 The Big Brawl (3)
- 26. Episode 26 The Big Brawl (4)
Season 3 (26 episodes)
- 1. Episode 1 Space Invaders (1)
- 2. Episode 2 Space Invaders (2)
- 3. Episode 3 Space Invaders (3)
- 4. Episode 4 Worlds Collide (1)
- 5. Episode 5 Worlds Collide (2)
- 6. Episode 6 Worlds Collide (3)
- 7. Episode 7 Touch and Go
- 8. Episode 8 Hunted
- 9. Episode 9 H.A.T.E
- 10. Episode 10 Nobodys Fool
- 11. Episode 11 The Lesson
- 12. Episode 12 The Christmas Aliens
- 13. Episode 13 New Blood
- 14. Episode 14 The Darkness Within
- 15. Episode 15 Mission of Gravity
- 16. Episode 16 The Entity Below
- 17. Episode 17 Time Travails
- 18. Episode 18 Hun on the Run
- 19. Episode 19 Reality Check (1)
- 20. Episode 20 Across The Universe (2)
- 21. Episode 21 Same As It Never Was (3)
- 22. Episode 22 The Real World (1) (4)
- 23. Episode 23 The Real World (2) (5)
- 24. Episode 24 Bishops Gambit
- 25. Episode 25 Exodus (1)
- 26. Episode 26 Exodus (2)
Season 4 (26 episodes)
- 1. Episode 1 Cousin Sid
- 2. Episode 2 The Peoples Choice
- 3. Episode 3 A Wing And A Prayer
- 4. Episode 4 Sons Of The Silent Age
- 5. Episode 5 Dragons Brew
- 6. Episode 6 I, Monster
- 7. Episode 7 Grudge Match
- 8. Episode 8 All Hallows Thieves
- 9. Episode 9 Bad Day
- 10. Episode 10 Aliens Among Us
- 11. Episode 11 Dragons Rising
- 12. Episode 12 Still Nobody
- 13. Episode 13 Samurai Tourist
- 14. Episode 14 The Ancient One
- 15. Episode 15 Scion of the Shredder
- 16. Episode 16 Prodigal Son
- 17. Episode 17 Outbreak
- 18. Episode 18 The Trouble With Augie
- 19. Episode 19 Insane in the Membrane
- 20. Episode 20 A Tale of Master Yoshi
- 21. Episode 21 Return of Savanti (1)
- 22. Episode 22 Return of Savanti (2)
- 23. Episode 23 Adventures in Turtle-Sitting
- 24. Episode 24 Good Genes (1)
- 25. Episode 25 Good Genes (2)
- 26. Episode 26 The Ninja Tribunal
Season 5 (12 episodes)
- 1. Episode 1 Lap of the Gods
- 2. Episode 2 Demons and Dragons
- 3. Episode 3 Legend of the Five Dragons
- 4. Episode 4 More Worlds Than One
- 5. Episode 5 Beginning of the End
- 6. Episode 6 Membership Drive
- 7. Episode 7 New World Order (1)
- 8. Episode 8 New World Order (2)
- 9. Episode 9 Fathers And Sons
- 10. Episode 10 Past Present
- 11. Episode 11 Enter the Dragons (1)
- 12. Episode 12 Enter the Dragons (2)