Super 3D Noah's Ark originally began development as a game based on the Clive Barker movie Hellraiser. Wisdom Tree acquired the rights to make a game based on the film for $50,000, and licensed the Wolfenstein 3D engine from id Software, believing that the Wolfenstein 3D engine and the first-person shooter genre would be a good match for the license. Development for the game began on the original NES, using a cartridge equipped with a co-processor that would have tripled the processing speed of the NES to allow the game to run fast enough. However, development of this version was halted because Wisdom Tree could not work around the NES' strict palette limitations, and because the cartridge itself would have been prohibitively expensive, with an estimated cost of $100 per cartridge for the consumer. Wisdom Tree then allowed their Hellraiser license to expire, and instead retooled the game for the SNES as Super 3D Noah's Ark.

In the source code of Super Noah's Ark 3D, an image from an alpha build of Doom can be found, despite the game being built off of the earlier Wolfenstein 3D's engine and not Doom's.