Martin Hollis, the director of GoldenEye 007 and Perfect Dark, described the development of the game in an interview with Retro Gamer magazine. He explained that Rare rejected the prospect of working on the GoldenEye sequel Tomorrow Never Dies “without hesitation”, as the development team felt they had spent too much time immersed in the James Bond universe. The decision to make the central character a woman was part of Hollis’ belief that there “should be more games centred on women”. To this end, the team created Joanna Dark, influenced by a number of other fictional heroines: Kim Kimberly from Level 9 Computing’s text adventure Snowball, the seductive spy Agent X-27 in 1930s film Dishonored, the eponymous femme fatale of the film Nikita, and FBI agent Dana Scully from television series The X-Files. The name “Joanna Dark” was taken from the French pronunciation of Joan of Arc as “Jeanne d’Arc”.

Ghost in the Shell was a major influence on the character, setting and plot. The name of the in-game company “dataDyne” was inspired by Yoyodyne from The Crying of Lot 49 by Thomas Pynchon. Another significant influence on the game’s locations was the work of author Philip K. Dick. Hollis explained that he and designer David Doak “picked a range of locations we thought would be impressive and architectural, on the model of GoldenEye but sci-fi dystopias.… The settings came first; the plot was then constructed by Dave to sew them together”. The word “Dark” was chosen for its association with the game’s bleak focus on killing. Hollis has noted the similarities to Criterion Software’s naming of Black: “Game developers just like black, nihilism, dystopian futures, the number zero, infinity, spheres, perfection—all that kind of stuff.” The “double slash” symbol in the game’s logo was inspired by the Japanese dakuten mark.

At one time Nintendo of Japan considered releasing the game there under the title 赤と黒 (Aka to Kuro, lit. Red and Black?). “Perfect Dark” does not translate well into Japanese, and the title “Red and Black” was considered sufficiently edgy. However, it was eventually released as パーフェクト・ダーク (Pāfekuto Dāku, パーフェクト・ダーク?), a transliteration of the Western title.

Despite popular belief Joanna’s hair color was never meant to be brown but always red. This can be seen in renders done by Rare. The devs have claimed this is due to the limitations of the N64.