"Flower, Sun, and Rain" was developed by Grasshopper Manufacture. The game was conceived by studio founder Goichi Suda, beginning development in 1999 after completion of the studio's debut title "The Silver Case". The staff number for "The Silver Case" was under ten people and thus they had to adjust their development goals based on that. For "Flower, Sun, and Rain" five or six more people were involved and thus the scope was increased, such as including exploration and action elements. According to Suda, "Flower, Sun, and Rain" was part of the studio's transition towards more action-oriented titles. While "The Silver Case" was published on the original PlayStation, that console was nearing the end of its viable life cycle, so "Flower, Sun, and Rain" was developed for the PlayStation 2 (PS2). "Flower, Sun, and Rain" moved away from the purely text-driven structure of "The Silver Case", but it still carried over many of the previous game's themes and concepts. As with "The Silver Case", Suda wanted to include puzzles, but felt that he had gone too far with the variety and challenge of puzzles within "The Silver Case". Instead, Suda created a single puzzle system revolving around numerical combinations, which both simplified puzzles and tied in with Mondo's character.