New characters
MK4 introduced:

* Fujin, god of Wind, ally of Raiden. First appeared in Mortal Kombat Mythologies: Sub-Zero as the second boss character.
* Jarek, the last of the Black Dragon Clan.
* Kai, a Shaolin monk and friend of Liu Kang.
* Quan Chi, a mysterious evil sorcerer. First appeared in Mortal Kombat Mythologies: Sub-Zero as the main antagonist.
* Reiko, Shinnok's general.
* Shinnok, an imprisoned Elder God. First appeared in Mortal Kombat Mythologies: Sub-Zero as the final boss.
* Tanya, a traitor to Edenia. She was rumored to be a glitched yellow female ninja from Ultimate Mortal Kombat 3.

MK4 also included the following hidden characters:
* Noob Saibot
* Goro
* Meat, a bloody skeleton.

Returning characters
* Liu Kang
* Jax Briggs
* Johnny Cage
* Raiden
* Reptile (now with his mask removed)
* Scorpion
* Sonya Blade
* Sub-Zero

Goro, not featured in the arcade version of MK4, was added as a sub-boss for the console versions of the game.

Boss and sub-boss
* Shinnok
* Goro