In the game's opening sequence, the U.S. version has the story text shifted to the left, however in the European release the text is centered.

The player was once able to fly in the game; both flight pads and red feathers appeared in earlier builds of the game.

The game originally began development in 1999 as a side-scrolling platformer for the Game Boy Color under the title "Banjo-Kazooie: Grunty's Curse". It would have featured Gruntilda putting a curse on Kazooie, and carrying her in a backpack, similar to Banjo. Production the game lasted only a few months before being halted later that year, and was restarted after Nintendo released the Game Boy Advance, eventually releasing as Banjo-Kazooie: Grunty's Revenge.

Eight games developed by Rare for the Game Boy Color and Game Boy Advance feature a recurring Easter egg: a crude drawing of a bovine eating a flower. Dubbed the "Rare Cow", it made its first known appearance in Conker's Pocket Tales in 1998, and last appeared in It's Mr. Pants in 2004.