Rinne Rokudou has bigger problems than going to school—namely, helping spirits pass over to the next life. Because of this responsibility, he often finds himself short on money and struggles to buy his necessities: food, clothes, and exorcism tools.

Sakura Mamiya has been able to see ghosts since she was little. She hoped she would outgrow it, but even after starting high school, nothing has changed. To make matters worse, the first time her ever-absent classmate, Rinne, shows up for school, only Sakura can see him. She assumes, as anyone would, that he is a ghost. However, to Sakura's surprise, Rinne proceeds to attend school like normal the next day. Kyoukai no Rinne chronicles Sakura's journey as she learns of Rinne's true nature and the existence of a hidden supernatural world.