The story of Kodomo no Jikan is centered around 23-year-old Aoki Daisuke, who has just landed his first teaching job as a grade school teacher at Futatsubashi Elementary School. He is placed in charge of Class 3-1, where one of his students, a mischievously precocious Rin Kokonoe, develops a crush on him and goes so far as to proclaim herself Aoki's girlfriend. She aggressively pursues her efforts to be with her teacher despite the fact that he will lose his job if she gets too close, a situation further complicated by the often complex, intertwining relationships existing between them and their respective friends, families, and peers.