New player characters:
- Cyrax (Sal Divita) – Yellow-colored Lin Kuei cyber assassin, and second of the three cyber assassins.
- Kabal (Richard Divizio) – Former Black Dragon warrior.
- Nightwolf (Sal Divita) – Native American shaman.
- Sektor (Sal Divita) – Red-colored Lin Kuei cyber assassin and also the first of the three cyborgs.
- Sindel (Lia Montelongo) – Resurrected Queen of Edenia who is being controlled by Shao Kahn. Sindel was originally named Mushasha in the early versions of the game.
- Sheeva (stop motion) – Female Shokan whose loyalty lies in the hands of Shao Kahn, and is also the protector of Sindel.
- Stryker (Michael O’Brien) – Riot control officer.
Returning player characters:
- Jax (John Parrish) – Special Forces major who works with Sonya to apprehend Kano.
- Kano (Richard Divizio) – Black Dragon thug who escaped arrest by Sonya and Jax.
- Kung Lao (Tony Marquez) – Shaolin monk who seeks to stop what Kahn is planning.
- Liu Kang (Eddie Wong) – Returning Mortal Kombat champion.
- Sonya Blade (Kerri Hoskins) – Special Forces lieutenant setting out again to capture Kano.
- Sub-Zero (John Turk) – Rogue Lin Kuei ninja who fled the clan after refusing to be converted to a cybernetic unit.
- Shang Tsung (John Turk) – Shao Kahn’s devious sorcerer.
- Smoke (Sal Divita) – Indigo-colored cyber assassin from the Lin Kuei and last of the three cyborgs, who was once a close friend of Sub-Zero (unlocked by the Ultimate Kombat Kode).
- Motaro (stop-motion) – A Centaur and the game’s sub-boss.
- Shao Kahn (Brian Glynn, voiced by Steve Ritchie) – Emperor of Outworld and the game’s final boss.
Although the game’s manual states both boss characters are unplayable, both Motaro and Shao Kahn can be enabled via secret cheat menus in the SNES and Genesis versions of the game. Noob Saibot (Richard Divizio) also returns as a hidden opponent.