According to producer Shohei Sakakibara in an interview with Famitsu, the team had originally considered a remake or reboot of the first game, Danganronpa: Trigger Happy Havoc. They had planned to change the story without changing the world or characters, but realized that because the plot of the first game was the "root" of all the future games, changing it would have too great of an impact on the series as a whole. As a result, they decided to remake the second game instead, as it allowed them to create a new Danganronpa game without "destroying the game world".

The game was originally scheduled to release in 2026, but was later delayed to 2027. According to series creator Kazutaka Kodaka and producer Shohei Sakakibara, this delay was done to give more development time, and to avoid competing with the release of Grand Theft Auto VI, which Kodaka joked he would be too busy playing to work on the game.