Resident Evil Zero was originally planned for the Nintendo 64 in the year 2000. Rebecca is shown to wear a beret similar to Jill Valentine from Resident Evil 1, and Billy's facial features were totally different from his final design.

Most of the characters and settings from the Gamecube version are in the N64 version, like the opening fight on a moving train. It was in development during the last years of the N64, so instead of finishing it, Capcom scrapped the build and developed it for the GameCube.