The first seeds of what is currently known as Genei Ibun Roku #FE were planted by a DSiWare photo application.

In an interview with Gamespot about the Shin Megami Tensei / Fire Emblem crossover, it was revealed that the project began while Atlus and Nintendo were working on a decorative photo application for Japanese DSiWare. One of the Nintendo employees on the project was a huge Shin Megami Tensei fan and pitched the idea, but Atlus had to decline at the time due to other commitments.

The idea would be revived shortly thereafter and quickly announced in January 2013. Originally the plan was to create something closer to Fire Emblem as a turn-based strategy game, which Atlus had some experience with in the Devil Survivor games, but the game shifted more toward its current incarnation as Nintendo wanted something that would play to Atlus's strengths.