Tomo-chan wa Onnanoko! follows Tomo Aizawa and Junichirou “Jun” Kubota, two childhood friends whose bond has been shaped by years of training together, hanging out after school, and growing up side by side with an easy familiarity that makes them seem inseparable to everyone around them. Tomo has been in love with Jun for a long time, but Jun still treats her like one of the guys and remains completely unaware of the feelings she is trying to keep hidden.
When their first year of high school begins, Tomo decides that she can no longer stay silent and finally confesses, only to learn that making Jun see her as a girl will not be simple. Her tomboyish habits, rough manner, and habit of answering problems with a punch only widen the gap between the way she sees herself and the way he sees her. As their school life goes on, Tomo keeps pushing Jun out of his comfort zone, trying to break through years of habit and force him to notice what has always been right in front of him. The result is a stubborn, lighthearted battle between friendship and romance, where every day becomes another chance to turn a lifelong friendship into something more without losing what made it special in the first place.