The green planet Peppy's Arwing is shown hurdling towards in the prologue for Star Fox 64 (and also its 3DS remake, Star Fox 64 3D) is actually meant to represent Papetoon, his and also Fox and James' home planet. The Japanese prologue even refers to it as such, and various Japanese SF64 material also mention it. However, when Star Fox 64 was localized for Western audiences, Nintendo of America completely wiped out all specific mention of Papetoon in both the prologue and also manuals/guidebooks.

One of Peppy's most well known lines, "Never give up. Trust your instincts.", was added because one of the developers, Mitsuhiro Takano, wasn't very good at the game and wanted to get some encouragement.

In the Japanese Versions of the game, after being shot down one of Fox's Teammates will shout out his name, similar to Star Fox Assault, but in the Western Versions, they instead shout "No!!!".

The game's opening features the phrase "Star Fox in Nintendo 64". This was a translation error and is supposed to read "Star Fox on Nintendo 64". This was fixed in the 3DS remake.

In the European version, there is an extra language called "Lylat", a made up language which is similar to the gibberish spoken in the original Star Fox.

In the Japanese version, the character icons do not sync with their voices and simply animate the whole way. This was changed in the western versions of the game where the icons would sync with what the characters are saying.

If the player takes too long to defeat the Golemech boss at the end of Venom's easy path (about seven minutes), the fight will end and the player will run into a wall, killing themselves and making the fight restart.

In the Macbeth level, there is a time limit to fighting the boss even if the player missed the Supply Depot ending that leads to Area 6. If the player gets far enough, the boss will state that the player was too slow, and dive bomb the player, killing them instantly. If using a cheat to have infinite health, then the boss will continue to bounce the player upwards until the game crashes.

On the title screen, you can use the analog stick to move the "64" part of the logo around. Fox and his crew will watch it as it moves.

The planet of Katina is a clear reference to the movie "Independence Day". Similar to the movie, you have to dog fight aliens that are invading the world and if you do not finish off the mother ship in time, it will destroy the base with a blue laser. The new partner you get in this fight, Bill Grey, is a reference to the General William Grey from the movie.

The way the characters in the game talk by opening and closing their mouths was inspired by Thunderbirds and other "English puppet dramas" (called "Supermarionation" by Thunderbirds co-creator Gerry Anderson). Shigeru Miyamoto was a fan of these shows and imagined that if the Star Fox series became popular enough, AP Films themselves would come from England to talk about turning it into a "puppet drama".

After obtaining a gold medal on all levels, Expert mode will be unlocked. In Expert mode, Fox wears his father James McCloud's glasses.

The robot boss of Sector X, dubbed "Spyborg" in the English version of Star Fox 64, is known as HVC-09 in the Japanese version.

HVC (Home Video Computer) was the model number that was used for Famicom (the Japanese equivalent to the Nintendo Entertainment System) hardware and peripherals. For example, the model number for R.O.B. (who in Japan was called Family Computer Robot) was HVC-012. Likewise, the model number for the NES Zapper (known as the Famicom Light Gun in Japan) was HVC-005. The model number for the Famicom itself was HVC-001.

Funny enough, in real life, there never was any NES related hardware whose model number was HVC-09.