Kodomo no Jikan's story revolves around a male twenty-three year old grade school teacher named Daisuke Aoki employed at Futatsubashi Elementary School (双ツ橋小学校, Futatsubashi Shōgakkō?). Daisuke is in charge of class 3-1, and one of his students, a mischievous young girl named Rin Kokonoe, has developed a crush on him, and has gone so far as to proclaim herself Daisuke's girlfriend. Rin continues her efforts to be with her teacher despite the fact that he will lose his job if she gets too close.

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