The elite all-boys boarding school Fujimori Academy has a long-standing and unusual tradition known as the Princess system. To boost school spirit and provide a sense of comfort in an environment without female students, three beautiful first-year students are selected each year to dress in Lolita-style costumes and act as the school's living idols. They perform at official functions, cheer for sports teams, and even have their own photo albums sold to the student body. In exchange for their duties, which are considered a full-time commitment, the chosen Princesses receive special privileges like exemption from certain classes and free meals.

The story focuses on three boys selected to be that year's Princesses. Yujiro Shihoudani is confident and enjoys the attention and perks that come with the role. Tooru Kouno is pragmatic and realistic, having accepted the position for its benefits. The third and central protagonist is Mikoto Yutaka, who is reluctant and embarrassed by the entire situation. Unlike his peers, Mikoto fiercely clings to his masculine pride and constantly looks for a way to escape his duties, causing friction and comedic situations as he is forced to participate.

Just as Mikoto begins to reluctantly accept his fate, a mysterious and handsome transfer student named Otoya Hanazono arrives. Otoya is sharply critical of the current Princesses, whom he views as half-hearted, and accuses the Student Council, led by the charismatic and calculating Shuuya Arisada, of neglecting the students' true wishes. To challenge the existing order, Otoya forms a rival group called the Dark Princesses, creating his own team of cross-dressing boys to compete for the students' affection and attention. He also announces his candidacy for the new Student Council, setting the stage for a power struggle over the school's future.

Caught in the middle of this conflict is Mikoto. He finds himself torn between his loyalty to his fellow Princesses, Yujiro and Tooru, and a strange, compelling attraction to the enigmatic Otoya. As the rivalry between the official Princesses and the Dark Princesses escalates, culminating in a heated election battle for control of the Student Council, Mikoto is forced to confront his own confused feelings. Through his friendship with Otoya and the escalating chaos, he ultimately comes to a new understanding of what it truly means to be a Princess, finally setting aside his personal pride to embrace the pride of the role.