Several hidden messages have a chance to appear, some in a garbled form, at the bottom of the screen upon beating the game. They were added in certain revisions of the arcade version of the game to fuel rumors and increase the number of quarters spent. These messages are:

• Who Is Smoke?
• Where Is Sonya?
• Who Is Jade?
• Where Is Kano?
• Friendship?
• Where Is Goro?
• Babality?
• Ceamr Odse Nto Exits (Ermac Does Not Exist)
• Emro Batmok Ot Meok (More Kombat To Kome)
• Sruep Ghih Miptac (Super High Impact)
• Three Rae On Stniiiaamel (There Are No Animalities)

The Sega Saturn port contains a single Redbook audio track on the game disc consisting of a discordant, high-pitched noise. Slowing this clip down to 15% of its original speed reveals that it is actually a poor-quality clip of a voice speaking indistinctly before a lengthy guitar riff plays. Because this track is not used anywhere in-game, it is unknown whether it is a leftover from development or if it was deliberately included as an Easter egg.

In Episode 7 of the TV series adaptation of The Last of Us, Ellie and Riley are seen playing the arcade version of Mortal Kombat II. At one point, Riley uses Mileena's fatality on Ellie's character Raiden, with Riley being heard pressing four buttons to initiate the killing blow. Following the episode's release, a number of fans online claimed this was inaccurate, as one can simply just press and hold the Heavy Kick command during the "Finish Him!" prompt to initiate her Fatality. However, other Mortal Kombat players argued that the show's display of gameplay could possibly be correct, pointing out that there is an alternate way to do the fatality. Specifically, Mileena can perform the Fatality by standing close to the opponent, holding the Block button and tapping the Heavy Kick command.

A secret Game Over screen exists that would rarely appear for a losing player. The screen features the "Goro's Lair" stage backdrop with a large red Roman numeral '3', seeming to foreshadow the then-in-production Mortal Kombat 3.

In Japan, the game was renamed to 'Mortal Kombat II: Ultimate Godly Fist'.

Johnny Cage's triple head uppercut fatality was inspired by a glitch in Mortal Kombat where you could preform his fatality twice, resulting in two heads being knocked off of the opponent instead of one.

In the Genesis port of the game, Rayden has an exclusive finisher that can be activated through a cheat, called "Fergality." This turns his enemy into a smoking version of Fergus McGovern, CEO of Probe Ltd. who worked on the port of the game.

An unused graphic of the WWF logo can be found within the game's code. It's likely that it was meant for an advertisement that was scrapped.

There is an unused animation of Raiden lifting up and shocking someone. It was likely a Fatality, as Raiden would eventually use a similar Fatality in Mortal Kombat 4.

The Japanese version of the SNES release is slightly censored. All blood has been recolored green and all fatality moves (excluding the stage fatalities) cause the screen to become monochrome.

Shao Kahn had to be re-sized to be taller than the other Kombatants, as his actor, Brian Glynn, was shorter than everyone on set.

By playing 250 matches in a row, the players unlock the ability to play a round of Pong in the middle of the match. The game lasts until one player gets 7 points before throwing both players back into the match.

In the Pit II level, there are two characters fighting in the background. Fans named them Hornbuckle and Torch. In actuality, they are just resized and recolored Liu Kang sprites. Torch would later appear as Blaze in Mortal Kombat: Deadly Alliance.

Kintaro was originally designed to be a playable, anthropomorphic tiger. However, he was changed to a Shokan like Goro due to the difficulty in creating a fur-lined costume.

In Armageddon and beyond, his design has changed to give him a more feline appearance, including fur and elongated teeth.