| Super Shredder (12 variants) | 83 |
| Stomped by the Foot (12 variants) | 82 |
| Stockman, Mad Fly-entist (12 variants) | 54 |
| Squirrelanoids (12 variants) | 81 |
| Splinter's Technique (12 variants) | 80 |
| Splinter's Technique (12 variants) | 233 |
| Splinter, Radical Rat (12 variants) | 169 |
| Splinter, Radical Rat (12 variants) | 251 |
| Splinter, Hamato Yoshi (12 variants) | 79 |
| Spicy Oatmeal Pizza (12 variants) | 109 |
| South Wind Avatar (2 variants) | 269 |
| South Wind Avatar (12 variants) | 78 |
| Slithering Cryptid (12 variants) | 168 |
| Slash, Reptile Rampager (12 variants) | 108 |
| Slash, Reptile Rampager (12 variants) | 208 |
| Skateboard (12 variants) | 178 |
| Shredder's Technique (12 variants) | 77 |
| Shredder's Technique (12 variants) | 232 |
| Shredder's Revenge (12 variants) | 76 |
| Shredder's Armor (12 variants) | 75 |
| Shredder, Unrelenting (12 variants) | 74 |
| Shredder, Unrelenting (12 variants) | 210 |
| Shark Shredder, Killer Clone | 320 |
| Shark Shredder, Killer Clone (2 variants) | 268 |
| Shark Shredder, Killer Clone (12 variants) | 73 |
| Sewer-veillance Cam (12 variants) | 53 |
| Saved by the Shell (12 variants) | 132 |
| Savanti Romero, Time's Exile (12 variants) | 72 |
| Savanti Romero, Time's Exile (2 variants) | 267 |
| Sally Pride, Lioness Leader (12 variants) | 225 |
| Sally Pride, Lioness Leader (12 variants) | 24 |
| Rocksteady, Crash Courser (12 variants) | 131 |
| Rock Soldiers (12 variants) | 107 |
| Return to the Sewers (12 variants) | 52 |
| Retro-Mutation (12 variants) | 51 |
| Renet, Temporal Apprentice (12 variants) | 202 |
| Renet, Temporal Apprentice (12 variants) | 50 |
| Ray Fillet, Man Ray (12 variants) | 49 |
| Ravenous Robots (12 variants) | 106 |
| Ravenous Robots (2 variants) | 271 |
| Rat King, Verminister (2 variants) | 266 |
| Rat King, Verminister (12 variants) | 71 |
| Raphael's Technique (12 variants) | 237 |
| Raphael's Technique (12 variants) | 105 |
| Raphael, Tough Turtle (12 variants) | 104 |
| Raphael, the Nightwatcher (12 variants) | 213 |
| Raphael, the Nightwatcher (12 variants) | 103 |
| Raphael, the Nightwatcher | 297 |
| Raphael, the Nightwatcher | 287 |
| Raphael, Ninja Destroyer (12 variants) | 218 |