At Momoyama High School, an all-girls school, the blunt and outgoing Chitose Hayami meets the timid and cute Yae Sakura when she offers to help her separate trash that was put in the wrong bin. Admiring Yae's kind heart, Chitose nominates the two as class representatives against Yae's will.

Later that day, to Yae's surprise, Chitose confesses her feelings to the former, telling her that she resembles her first love. In return, Yae explains that she was rejected by her middle school crush, a girl, and therefore hates being a girl herself. Chitose replies that she loves Yae the way she is. Enraptured by the sentiment, Yae begins to spend more time with Chitose.

Centered around the relationship that blooms between the two girls, Hanjuku Joshi explores the depth of human sexuality and the way adolescents view themselves and each other.

[Written by MAL Rewrite]