Kazutaka Kodaka began planning Master Detective Archives: Rain Code in 2016, while he was still working at Spike Chunsoft. It was designed to be different from the Danganronpa series, with a dark fantasy setting influenced by the works of Tim Burton. It also uses full 3D models throughout the game, as opposed to Danganronpa's blend of 3D environments and 2D characters: it does, however, still feature a similar psycho-pop aesthetic with neon colors.

When creating Kanai Ward, Kazutaka Kodaka originally considered giving it an original language, but dropped the idea when he realized it would be too "fantastical". Instead, he incorporated multiple languages (such as Russian, Hindi, Japanese and English, as well as other multi-nationalistic elements) on the signboards around town. This inspired him to make the various character names multinational as well, assigning names in a way that the characters would fit them. At the same time, however, Kodaka avoided using typical names for the cast, instead opting for more unusual names such as "Hellsmile" and "Nightmare": words that are commonly heard, but not as names given to somebody. He specifically went for names that were unique but easy to remember.

In regards to the character Makoto Kagutsuchi, who has a normal sounding name despite his unique design, Kodaka stated:

Despite appearing in the Japanese version of the "World Detective Organization Character Trailer Pt. 2" video released to promote the game, the character Yakou Furio is absent from the English version, despite both trailers being near-identical otherwise.