Bokuhime Project is a single-player mystery adventure game in which the player takes the role of a young man who infiltrates a school for refined young ladies to investigate an incident. As part of the investigation, the player aims to improve their character’s cuteness to get a seat in a school organization, and to interact with characters including the currently elected students in the organization while maintaining their composure.

To do so, the player takes part in cross-dressing lessons called “Bokuhime Project” to improve three character statistics – Visual, improving feminine appearance; Culture, increasing knowledge as a woman; and Spirit, increasing resistance to feeling ashamed – and partakes in various activities including swimming lessons, tea parties, cosplay, and physical education, to increase their character’s femininity; some such training activities unlock character customization options, such as the option to wear a maid costume after training at a maid café. When the player character’s statistics are high enough, the player can play the Girl’s Emotion Mode, where they go on stage and answer questions based on their experience and training to increase the student body’s support for the player character. If they fail, the character Akira gives hints on how to make progress.