Chitose Hayami, a sociable and truthful student at Momoyama High School - an all-girls school - assists the introverted and lovable Yae Sakura in waste segregation. Yae's compassionate character impresses Chitose, who then nominates both of them as class representatives, despite Yae's hesitation.
Later on, Chitose confesses her feelings for Yae and discloses that Yae reminds her of her past lover. Yae, in turn, shares that her middle school crush was on a girl who turned her down, causing her to dislike her feminine side. Notwithstanding, Chitose pledges to cherish Yae exactly as she is, catching Yae's interest and establishing a deeper bond between them.
The plot of Hanjuku Joshi revolves around the relationship between these two young women, as well as the exploration of teenage sexuality and self-awareness.