Bokuhime Project is a mystery adventure video game developed by Wizard Soft and published by Nippon Ichi Software. The player takes the role of a young man who infiltrates a school for refined young ladies by enrolling as a female student to investigate an incident involving his sister. As part of their investigation, the player aims to get a seat in an influential organization at the school, and thereby needs to improve their character statistics to raise their character's cuteness, overcoming the other candidates.

The story follows Minato Ikusa, who infiltrates Yuriai Private Academy – a school whose student body consists of 99% women – to save his sister Marika who has fallen into a coma after being involved in an incident at the academy, which Yuriai tries to cover up. To do so, he takes his cousin Akira's place at the school while she stays at home, and enrolls as a female student under the name Erika; he additionally attends the school on the boys' side as Minato, living a double life. At the school, there is an organization known as the Four Princesses, which wields considerable influence; Ikusa aims to get a seat in the organization to investigate the incident his sister was involved in, and as such must work toward becoming the most beautiful woman in the school and winning the princess election, overcoming the other candidates and the current Four Princesses. Akira, who is very knowledgeable in male-to-female cross-dressing, helps Ikusa with this, training him in "cross-dressing skills".

Among major characters are Hiyu Shinosaki, a student who supports Ikusa and sees him as a sister, and who is attracted to women; and the misogynist Ouga Rokujou, a student who is the representative of a major company. The students in the Four Princesses include the gyaru princess Lira Hoozuki, a charismatic model; the shrine maiden princess Uran Ryuguuin, a yamato nadeshiko who has been isolated from the world; the imperial princess Hermes Himegami, who appears friendly with Ikusa; and the knight princess Daria Himegami, the protective older sister of Hermes who was friends with Ikusa's sister. Nemesia Himegami, the school director and the mother of Hermes and Daria, also appears, giving Ikusa advice.