In the Japanese version, both Peach and Bowser's victory screen show them drinking the victory champagne, with Peach even having a red face, showing that she is drunk. This was changed to have Bowser just holding the bottle and Peach throwing it up in the air.

The background used on the title screen in the Japanese version has what appears to be an Ai-Ai Gasa (or Love-Love Umbrella) saying "Mario" and "Peach", and "Mario Kart" written in Japanese. These were removed in the international version, and the mushroom was moved.

A news story from the November 1992 issue of Daily Yomiuri (a part of Japan's largest media conglomerate) claimed that Luigi was actually evil:

The official handbook actually encourages players to look at their opponents' screens, an action usually frowned upon in the gaming community.

Development of the game began with the idea of making a two-player racing game following F-Zero, which only had a single player mode. The game's prototype originally only had a generic "guy in overalls". The decision to include Mario characters was made roughly three to four months into development after the developers decided to add Mario driving one of the karts because they were curious about how the game would look. They ultimately decided the game looked better, and thus made the game a Mario series title.

A prototype of the game has animations when ranking 2nd or 3rd place in a championship, that don't appear within the final game. Scoring 2nd shows a Super Koopa looping over the podium and then getting hit by the winner's champagne cork, whilst the 3rd place animation has a group of Koopa Paratroopas flying over the podium, the last of which is also hit by the cork.

In the Japanese release, a Boo sound is played when you unlock the Special Cup by pressing L, R, L, R, L, L, R, R, A on the Time Trial menu. This unlock method works in the international release as well though the Boo sound does not play.

According to Nintendo, in a developer's interview, Donkey Kong Jr. was added because of both the 10th anniversary of his debut game, and that his shirt was easy to design.

The game has a secret CPU ghost mode which can be accessed under the Time Trial menu by pressing Start on a controller in port 2 while selecting a driver. This triggers a CPU cursor to appear, allowing the player to select a ghost driver to compete against. However, the CPU ghosts are capable of interacting with elements of a track's mechanics, like the ice blocks found in Vanilla Dome.

If the player allows the CPU to destroy these blocks, then drives over where the blocks were, then saves and race against their own ghost, a glitch will occur where the ghost will vanish when it touches the block that was supposed to have been destroyed and trigger a visual error where the player's tires will cycle between two frames of animation even while in an idle position. This glitch only occurs when the player and the ghost use the same driver.