Ecchi na no wa Watashi no Sei ja Arimasen follows the daily life of a high school girl who possesses a unique and troublesome constitution that causes her to emit a special pheromone. While entirely innocent and unaware of the effect she has, this pheromone inadvertently triggers intense and exaggerated ecchi situations with those around her, primarily her male classmates and teachers. Instead of being seen as the victim of these accidents, she is constantly blamed for provoking them, leading to the core conflict of the story.

The main protagonist is a kind-hearted but unfortunate girl who just wants a normal school life but is frequently forced to defend herself with the phrase that gives the series its title, insisting it is not her fault. The male lead is often a friend or classmate who is initially suspicious of her, believing she causes trouble on purpose, but he gradually learns the truth about her condition. A supporting cast of school authority figures, including a strict student council president and a disciplinary teacher, serves as the primary opposition, repeatedly punishing the protagonist for incidents they believe she orchestrates. Secondary characters include a small group of friends who are aware of her innocence but are often caught in the chaos.

The setting is a typical Japanese high school, featuring standard locations like the classroom, the school’s rooftop, the library, and the gymnasium storage shed, where many of the accidental incidents unfold. The narrative primarily follows a comedic episodic format where each chapter presents a new disaster for the protagonist. Major recurring narrative arcs include an introduction arc that establishes her constitution and the school's disciplinary system, a summer vacation arc where the confined setting of a study camp or beach trip escalates the accidental incidents, and a cultural festival arc where public performances and crowded hallways create maximum chaos for her. A later arc often involves a group of outcast students who try to exploit her power for their own benefit, forcing the male lead and her friends to work together to protect her.