The game started out more or less as a direct port of the original Kingdom Hearts Coded. When it was found that the game didn't fill up all of the cartridge's memory, the development team was asked to make it "full 3D and put in the panel system arrangement from Days."

Kingdom Hearts Re:Coded was planned to be on Nintendo's Wiiware service, to be released in episodes, but was ported to the Nintendo DS due to the international popularity of the Nintendo DS, which would be more accessible to as many people as possible.

This game was supposed to use mugshots during dialogue scenes, as did Kingdom Hearts 358/2 Days, but they went unused. The final game uses full portraits instead, just like the original Japan-only Coded mobile game did.