Perfect Dark Zero was originally being developed as a Nintendo GameCube launch title, and made a small appearance at Nintendo's Spaceworld 2000 event, but was not completed in time. After Microsoft bought Rare, development was shifted to the Xbox, and later to the Xbox 360 to become a launch title for that console.

With Perfect Dark Zero being a prequel with a younger Joanna Dark, her design originally was more cartoony and exaggerated. Lead concept artist Will Overton was inspired by anime and manga, specifically "Ghost in the Shell", to give the game an art style more in line with Rare's other titles such as Banjo-Kazooie and Conker. Overton mentioned he wasn't a fan of her original design, though kept aspects such as her reddish hair and the colors of her Carrington Institute uniform. Lead background artist Sam Jones mentioned one of the biggest challenges was trying to maintain a middle ground between realism and the "Rare-ish" art style. The new design was first unveiled in 2002 via promotional renders included in press releases for Microsoft's acquisition of Rare, and was not well received by the public. The final game instead used more Western influences such as the films "Star Wars: Episode II - Attack of the Clones" and "Minority Report".