"Seito Kaichō no Yūutsu" centers around the student council of Hekiyou Academy, a prestigious all-girls school, and the challenges faced by its members. The narrative primarily revolves around the council president, Ayaka Narumi, who is admired for her beauty, intelligence, and leadership. Despite her seemingly perfect exterior, Ayaka harbors a deep-seated fear of men due to a traumatic childhood incident. This phobia complicates her interactions and responsibilities, particularly when the school transitions to a co-ed system, introducing male students into the previously all-female environment.

The story explores Ayaka's efforts to adapt to the changing dynamics of the school while maintaining her composure and authority. Her interactions with the male students, especially the kind-hearted and perceptive Takuto Kira, play a significant role in her character development. Takuto, who becomes aware of Ayaka's fear, strives to support her and help her overcome her anxieties, fostering a gradual bond between them.

Other key characters include the vice president, Kanade Izumi, who is fiercely loyal to Ayaka and often acts as her protector, and the secretary, Rino Endo, whose cheerful demeanor contrasts with the more serious tones of the council. The narrative delves into the personal struggles and growth of these characters, as well as their relationships with one another, against the backdrop of the school's evolving environment.

The series balances moments of humor, drama, and romance, with a focus on themes of overcoming fear, personal growth, and the complexities of human relationships. The student council's activities and the challenges they face serve as a vehicle to explore these themes, creating a narrative that is both engaging and reflective of the characters' journeys.