"Clean Freak! Aoyama-kun" centers on Aoyama, a high school soccer prodigy whose obsessive cleanliness and germaphobia shape both his personal life and athletic career. Despite his exceptional talent on the field, Aoyama’s compulsive need to sanitize himself and his surroundings often complicates his interactions with teammates and opponents. His meticulous routines, such as disinfecting his hands before touching the ball or avoiding physical contact with others, highlight his struggle to balance his passion for soccer with his overwhelming fear of contamination.

The narrative explores Aoyama’s relationships with his teammates, particularly his childhood friend Kaoru Zaizen, who serves as a grounding presence and often mediates between Aoyama’s quirks and the demands of team dynamics. The series delves into the challenges Aoyama faces in a sport that inherently involves physicality and unpredictability, emphasizing his determination to excel despite his unique limitations. Through various matches and interpersonal conflicts, the story examines themes of perseverance, teamwork, and self-acceptance, as Aoyama learns to navigate his anxieties while pursuing his love for soccer.

Supporting characters, such as the pragmatic team captain and other players, provide additional layers to the story, showcasing how Aoyama’s behavior impacts the team and how they, in turn, adapt to his needs. The series balances comedic moments stemming from Aoyama’s extreme cleanliness with heartfelt scenes that underscore his growth as both an athlete and an individual. By focusing on Aoyama’s journey, "Clean Freak! Aoyama-kun" offers a unique perspective on the intersection of personal challenges and competitive sports.