According to Shigeru Miyamoto in an edition of Iwata Asks regarding Star Fox 64 3D, Yusuke Amano originally wanted to create an all new Star Fox title for the Nintendo 3DS. However, the higher ups at Nintendo wanted a game that could be released fast for the 3DS' launch window in 2011, whereas a fully original title would require at least three years to make. Thus the project was reduced into a simplistic remake of Star Fox 64. Miyamoto called upon Dylan Cuthbert and Q-Games, who previously had worked on Star Fox Command in for the Nintendo DS in 2006, to assist development.

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.

The Western dub for Star Fox 64 3D notably brought back many of the original voice actors from the N64 version to reprise their respective roles for the first time in years, those being:

•Mike West (Fox, James)
•Lyssa Browne (Slippy, Katt, Spyborg)
•David Frederick White (R.O.B, Pigma, General Pepper, Attack Carrier Pilot)
•Ja Green (Leon, Shogun Pilot, Sarumarine Captain, Forever Train Conductor, Area 6 Commander)

For unknown reasons, David Frederick White goes uncredited.

The rest of the cast, however, were recasted:

•Falco, Andrew, Meteo Crusher Pilot, and Caiman, all originally voiced by Bill Johns, were now voiced by Mark Lund, Mike West, Jaz Adams and Jay Ward respectively.
•Wolf, Bill Grey and Granga, all originally voiced by Jock Blaney, were now voiced by Mike West, Jaz Adams and Mark Lund respectively.
•Peppy and Andross, both originally voiced by Rick May, were now voiced by Jaz Adams and David Frederick White respectively.