When Cruis'n USA was ported to the Nintendo 64, certain elements were censored. These included the ability to run over animals, which were removed from the game entirely, several unspecified Easter eggs, and a scene at the end of the arcade version. In this scene (set either on the roof of the White House or the Moon), then US president Bill Clinton is throwing a hot tub party in the back of a pick-up truck with bikini-clad models and some other men in suits; one of the models is then first lady Hillary Clinton. The Clintons, the hot tub, and the models were removed and replaced with the player's car on a turntable in the Nintendo 64 version. Director Eugene Jarvis spoke out against this censorship, stating: "It seems like they don't have any sense of humor. I don't know what's wrong with those people." According to a reader poll from IGN at the time, 54% of readers opposed these changes, while 13% supported them, and 13.3% sent letters complaining about the changes to Nintendo.

As part of a licensing deal between Midway and Nintendo, the arcade versions of Cruis'n USA and Killer Instinct were advertised both in their attract modes and on flyers as being powered by Nintendo's Ultra 64 hardware, which would eventually be released as the Nintendo 64. However, this claim was false; the versions of both games shown at the 1994 Summer Consumer Electronics Show ran on a modified JAMMA arcade board. As for the versions released to arcades, Cruis'n USA ran on the significantly different Midway V arcade hardware, while Killer Instinct only utilized parts of the Nintendo 64 hardware. It used a 64-bit MIPS CPU and the Nintendo 64 file format for data structure, but not the console's memory media or graphics technology.

The trophy girl who appears at the end of a race when finishing first place is adult film star Shyla Foxxx, who's credited in the game under her birth name, Anutza Herling. In the arcade version, she appears with a pink bikini top; in the Nintendo 64 version, a shirt with the game's logo on it was drawn over her sprites.