Princess Princess is a story revolving around the lives of three boys chosen to dress up as girls at the all-boy school they attend, which also just happens to be the most elite school in the area. The main protagonist, Tooru Kouno, has just transferred to a new all-boys school, Fujimori, after living with his uncle for a time. He is one such boy chosen to be one of the Hime (姫) or ＂Princesses＂, which is a tradition at the school in order to break up the monotony of life surrounded by nothing but males. Students (based on certain qualifications) are selected to be Princesses and are made to dress up as girls and attend school functions like this.

At the beginning of the story, there are already two such Princesses, Yuujirou Shihoudani and Mikoto Yutaka, known as the Western Princess and Eastern Princess respectively, due to their room location. Toru is convinced into becoming a Princess soon after entering the school though once he accepted the job, he found it to be much more enjoyable than he thought