Haruchika: Haruta to Chika wa Seishun Suru follows Chika Homura as she begins high school with a very specific goal: to cultivate a "cute girl" persona. Despite her all-star status, she quits the volleyball team and joins her school's underrated Wind Instrument Club, choosing the flute because she believes it is the most delicate and feminine instrument. There she reunites for the first time in nine years with her childhood friend Haruta Kamijou, whose personality is the complete opposite of her own. Chika's efforts to appear more endearing do not fool Haruta, but that does not stop her from developing a crush on the band's instructor, Shinjirou Kusakabe—only to learn that Haruta likes him too.
Chika's high school life does not unfold the way she imagines, as mysteries begin appearing around her and her friends. While trying to recruit enough members for musical competitions, the club members work together to investigate the incidents troubling their school. The series ties its school-band comedy and light romance to a string of small mysteries, centering on the uneasy partnership between Chika and Haruta as they balance rehearsals, rival feelings, and the effort to keep the club going.