The Wii U Virtual Console port of the game has the option to select both Multiplayer and Ghost Exchange. However, both options are locked out due to the physical game requiring the Game Boy Advance Game Link Cable, which unlocks those game modes on the actual Game Boy Advance hardware.

An unused test course can be found stored in the game's memory. Its mini-map resembles the Peach Circuit track, and has no AI routes for CPU drivers. It uses the same background music that plays in Peach Circuit, Luigi Circuit, and Mario Circuit.

The earlier version of the zipper did not flash.

Mario Kart: Super Circuit is the first game in the series to feature a Lightning Cup. It is also the only Lightning Cup with original stages, as from Mario Kart DS onward, it only featured stages from previous Mario Kart games.

Despite the Monty Moles from Donut Plains 2 and 3 being removed, the holes they pop out from were still updated with new graphics in the tracks' tileset.

Sky Garden is the only course in the Mario Kart series that appears in the same cup in two different games.

Triple Bananas, Golden Mushrooms, Fake Item Boxes and Bo-ombs were all going to return as items but were cut for uknown reasons. Their sprites can still be found in the game's data.

Both during gameplay and inn the preview image to the track Sunset Wilds, the Shy Guys wear Native American headdresses in the Japanese release. These were removed in the International release.

Bowser's Castle from Paper Mario makes a small cameo in the Rainbow Road course.

There are Tilemaps and Minimaps for all of the battle courses from Super Mario Kart. While these might have only been used as placeholders before the new ones were completed, it may also have also been possible to unlock these courses just like the tracks at one point. These are all stored in one piece, unlike the rest of the tracks and battle courses, which are stored in chunks.

In the Japanese version of Mario Kart 64, instead of the announcer and menu options being voiced by Mario they are instead voiced by the same VA who played the announcer in Wave Race 64: John Hulaton.

According to Hulaton in an interview with DidYouKnowGaming?, after recording his lines for Wave Race 64 he was handed a slip of paper and was then told to record the lines on it without being told what it was for. These lines ended up being for Mario Kart 64. Hulaton's agent was reportedly very upset, as Hulaton was not paid for these lines and on top of that his name was misspelled as 'John Huraton' in the credits.

The lines he recorded would then later be used in the Japanese and International versions of Mario Kart: Super Circuit, where he remained uncredited.