Unlimited continues
Press Up, Up, "Toward", "Toward", "Away", "Away", Down, Down while the game loads. Shao Khan say "Excellent" to confirm correct code entry.
Question mark menu
Press "HP", "LP", "LK", "HK", "Block", "Block", "Run", "Run", "Block", "Block" when the story introduction is displayed. The phrase "You will never win" will be spoken to confirm correct code entry. Press [Up] when the Mortal Kombat 3 logo and cube appears to display the question mark option.
Cheat codes
Start the game by using one of the following command line parameters to activate the corresponding cheat function. Note: Multiple codes may be entered at once.
| Effect | Parameter |
| Short fighters | 54321 |
| Very thin fighters | 1111 |
| Fat fighters | 8888 |
| Tall fighters | 12345 |
| Shadow fighters | 831 |
| Invisible combatants | 1995 |
| Turbo mode | 8000 |
| Slow mode | 603015 |
| Backwards Kombat | 9966 |
| Block causes 99% damage | 4862222 |
| Temporarily enable Smoke, with normal CPU | 666 |
| Temporarily enable Smoke, with hard CPU | 0666 |
| Temporarily enable Bosses in 2-player mode | 1000000 |
| Disables blood and fatalities | noblood |
| Enables blood fatalities | blood |
| Disables fatalities | noviolence |
| Enables fatalities | violence |
Ultimate Kombat Kodes
Perform a clockwise sweep of the controller to display the Ultimate Kombat Kodes screen. The icons on the bottom of the VS screen can be changed by pressing the HP, HK, and LK in that order. Player one selects the first three codes and player two controls the last three. When icons are placed in a certain combination, a Kombat Kode is revealed.
Then ten possible icons and number of button presses are:
0: Dragon
1: MK
2: Ying Yang
3: 3 Symbol
4: Question Mark
5: Lightning Bolt
6: Goro
7: Raiden
8: S. Khan
9: Skull
| Effect | Kombat Kode |
| No throws | 100-100 |
| No blocking | 020-020 |
| No power bars | 987-123 |
| Half energy for player 1 | 033-000 |
| Half energy for player 2 | 000-033 |
| 1/4 energy for player 1 | 707-000 |
| 1/4 energy for player 2 | 000-707 |
| Fight as Smoke | 010-696 |
| Dark fighting | 688-422 |
| Random morphing | 460-460 |
| Dark fighting, random morphing, no blocks, and no power bars | 985-125 |
| Unlimited run | 466-466 |
| Galaga | 642-468 |
| No Fear | 282-282 |
| "There is No knowledge that is not power" | 123-926 |
| Holds flippers during casino run | 987-666 |
| Winner fights Motaro | 969-141 |
| Winner fights Noob Saibot | 769-342 |
| Winner fights Shao Kahn | 033-564 |
| Winner fights Smoke | 205-205 |
| Player 1 heals after each hit | 101-000 |
| Player 2 heals up after each hit | 000-101 |