Season 1 (64 episodes)
- 1. Episode 1 A Real American Hero (1): The Cobra Strikes
- 2. Episode 2 A Real American Hero (2): Slave of the Cobra Master
- 3. Episode 3 A Real American Hero (3): The Worms of Death
- 4. Episode 4 A Real American Hero (4): Duel in the Devils Cauldron
- 5. Episode 5 A Real American Hero (5): A Stake in the Serpents Heart
- 6. Episode 6 The Revenge of Cobra (1): In the Cobras Pit
- 7. Episode 7 The Revenge of Cobra (2): The Vines of Evil
- 8. Episode 8 The Revenge of Cobra (3): The Palace of Doom
- 9. Episode 9 The Revenge of Cobra (4): Battle on the Roof of the World
- 10. Episode 10 The Revenge of Cobra (5): Amusement Park of Terror
- 11. Episode 11 The Pyramid of Darkness Part 1: The Further Adventures of G.I. Joe
- 12. Episode 12 The Pyramid of Darkness Part 2: Rendez-vous in the City of the Dead
- 13. Episode 13 The Pyramid of Darkness Part 3: Three Cubes to Darkness
- 14. Episode 14 The Pyramid of Darkness Part 4: Chaos in the Sea of Lost Souls
- 15. Episode 15 The Pyramid of Darkness Part 5: Knotting Cobras Coils
- 16. Episode 16 Countdown for Zartan
- 17. Episode 17 Red Rockets Glare
- 18. Episode 18 Satellite Down
- 19. Episode 19 Cobra Stops the World
- 20. Episode 20 Jungle Trap
- 21. Episode 21 Cobras Creatures
- 22. Episode 22 The Funhouse
- 23. Episode 23 Twenty Questions
- 24. Episode 24 The Greenhouse Effect
- 25. Episode 25 Haul Down the Heavens
- 26. Episode 26 Synthoid Conspiracy (1)
- 27. Episode 27 Synthoid Conspiracy (2)
- 28. Episode 28 The Phantom Brigade
- 29. Episode 29 Lights! Camera! Cobra!
- 30. Episode 30 Cobras Candidate
- 31. Episode 31 Money to Burn
- 32. Episode 32 Operation Mind Menace
- 33. Episode 33 Battle for the Train of Gold
- 34. Episode 34 Cobra Soundwaves
- 35. Episode 35 Where the Reptiles Roam
- 36. Episode 36 The Gamesmaster
- 37. Episode 37 Lasers in the Night
- 38. Episode 38 The Germ
- 39. Episode 39 The Viper is Coming
- 40. Episode 40 Spell of the Siren
- 41. Episode 41 Cobra Quake
- 42. Episode 42 Captives of Cobra (1)
- 43. Episode 43 Captives of Cobra (2)
- 44. Episode 44 Bazooka Saw a Sea Serpent
- 45. Episode 45 Excalibur
- 46. Episode 46 Worlds Without End (1)
- 47. Episode 47 Worlds Without End (2)
- 48. Episode 48 Eau de Cobra
- 49. Episode 49 Cobra Claws Are Coming to Town
- 50. Episode 50 An Eye for an Eye
- 51. Episode 51 The Gods Below
- 52. Episode 52 Primordial Plot
- 53. Episode 53 Flints Vacation
- 54. Episode 54 Hearts and Cannons
- 55. Episode 55 Memories of Mara
- 56. Episode 56 The Traitor (1)
- 57. Episode 57 The Traitor (2)
- 58. Episode 58 Pit of Vipers
- 59. Episode 59 The Wrong Stuff
- 60. Episode 60 The Invaders
- 61. Episode 61 Cold Slither
- 62. Episode 62 The Great Alaskan Land Rush
- 63. Episode 63 Skeletons in the Closet
- 64. Episode 64 Theres No Place Like Springfield (1)
Season 2 (30 episodes)
- 1. Episode 1 Arise, Serpentor, Arise! : Day 1
- 2. Episode 2 Arise, Serpentor, Arise! : Day 2
- 3. Episode 3 Arise, Serpentor, Arise! : Day 3
- 4. Episode 4 Arise, Serpentor, Arise! : Day 4
- 5. Episode 5 Arise, Serpentor, Arise! : Day 5
- 6. Episode 6 Last Hour to Doomsday
- 7. Episode 7 Computer Complications
- 8. Episode 8 Sink the Montana
- 9. Episode 9 Lets Play Soldier
- 10. Episode 10 Once Upon a Joe
- 11. Episode 11 The Million Dollar Medic
- 12. Episode 12 Cobrathon
- 13. Episode 13 The Rotten Egg
- 14. Episode 14 Glamour Girls
- 15. Episode 15 Iceberg Goes South
- 16. Episode 16 The Spy Who Rooked Me
- 17. Episode 17 Grey Hairs and Growing Pains
- 18. Episode 18 My Brothers Keeper
- 19. Episode 19 My Favorite Things
- 20. Episode 20 Raise the Flagg!
- 21. Episode 21 Ninja Holiday
- 22. Episode 22 G.I. Joe and the Golden Fleece
- 23. Episode 23 The Most Dangerous Thing in the World
- 24. Episode 24 Nightmare Assault
- 25. Episode 25 Second Hand Emotions
- 26. Episode 26 Joes Night Out
- 27. Episode 27 Not a Ghost of a Chance
- 28. Episode 28 Sins of Our Fathers
- 29. Episode 29 In the Presence of Mine Enemies
- 30. Episode 30 Into Your Tent I Will Silently Creep
Season 3 (24 episodes)
- 1. Episode 1 Operation Dragonfire - Part One
- 2. Episode 2 Operation Dragonfire - Part Two
- 3. Episode 3 Operation Dragonfire - Part Three
- 4. Episode 4 Operation Dragonfire - Part Four
- 5. Episode 5 Operation Dragonfire - Part Five
- 6. Episode 6 United We Stand
- 7. Episode 7 Revenge of the Pharoahs
- 8. Episode 8 Granny Dearest
- 9. Episode 9 Victory at Volcania - Part One
- 10. Episode 10 Victory at Volcania - Part Two
- 11. Episode 11 The Nozone Conspiracy
- 12. Episode 12 I Found you...Evy
- 13. Episode 13 Night of the Creepers
- 14. Episode 14 General Confusion
- 15. Episode 15 Stuck on You
- 16. Episode 16 Pigskin Commandos
- 17. Episode 17 Cold Shoulder
- 18. Episode 18 Injustice and the Cobra Way
- 19. Episode 19 The Mind Mangler
- 20. Episode 20 D-Day at Alcatraz - Part One
- 21. Episode 21 D-Day at Alcatraz - Part Two
- 22. Episode 22 An Officer and a Viperman
- 23. Episode 23 Thats Entertainment
- 24. Episode 24 BIOK
