In Japan, Danganronpa 2: Goodbye Despair and Danganronpa V3: Killing Harmony are known as "Super Danganronpa 2: Goodbye Despair Academy" and "New Danganronpa V3: Everyone's New Semester of Killing" respectively. According to Danganronpa 2 director Takayuki Sugawara, the "Super" prefix was chosen by the second game's staff to indicate that they wanted to improve and surpass the first game, having been inspired by Famicom and Super Famicom games they grew up playing. According to series creator Kazutaka Kodaka, the "New" prefix was added to Danganronpa V3's title to continue this trend in anticipation of the game's reveal at a Sony press conference in September 2015.

During the 16-bit era of video games, it was a regular practice for developers to include the adjective "Super" in the titles of sequels to older games for the same reasons it was added to Danganronpa 2, which expanded on the lore of the first game while changing other gameplay elements. In the modern era of video games, this trend evolved into adding the word "New" (新, "shin") instead to indicate that it is a new spin on an older game, which Danganronpa V3 did to show it was meant to be a new take on the series formula while being almost disconnected from the lore of previous games.

The final twist in the game, where it's revealed that Spoiler:the entire Danganronpa franchise was actually a reality television show spanning fifty-three seasons, was made with the intention to "bring a more interesting idea to the fans". As noted by Kazutaka Kodaka: