Seitokai Yakuindomo follows Takatoshi Tsuda, who on his first day at the formerly all-girls Ousai Private Academy is stopped by student council president Shino Amakusa for his untidy uniform. After apologizing for delaying him before his first class, and noting that the council needs a male point of view as boys begin attending the school, Shino appoints him vice president of the student council before he has even properly entered the building.
What should be a straightforward school life quickly turns into a constant barrage of absurd sexual jokes and deadpan teasing. Shino, who looks studious and serious but is secretly a huge pervert obsessed with erotic innuendo, leads the chaos with relentless enthusiasm. Secretary Aria Shichijou appears to be a sheltered young lady from a wealthy family, yet she is every bit as risqué as the president, if not more. Treasurer Suzu Hagimura seems comparatively normal, but she is deeply self-conscious about her elementary-school-sized body and cannot escape the others' teasing.
As Takatoshi tries to do his job and keep the student council functioning, he is swept into the unending madness of Ousai Private Academy, where every meeting becomes a new round of improvised lewd comedy and the group's bizarre chemistry only grows stronger.