This one's definitely different from all the other anime/manga out there. When talking about Kodomo no Jikan, the most important thing to get out of the way is to mention that it contains copious amounts of loli fanservice, i.e. little girls engaging in suggestive behavior. This alone dissuades many from watching it, as it did for me initially. However, Kodomo no Jikan's meaningful characterizations, character development, and social criticism sets it apart from the vast majority of anime, and the inappropriate behavior of the girls is vital to the questions the anime raises.
Take, for example, one of the first encounters between Kokonoe Rin, an elementary school girl, and her teacher, Daisuke Aoki, and the audience. Aoki discovers that Rin harassed and threatened the previous teacher to the point of illness. Rin accuses the previous teacher of doing the same to her friend, at which point Aoki tells Rin he must inform her parents of this. In response, Rin pulls down her panties and blackmails Aoki: "What do you think will happen if I screamed, 'Help' right now?"
In this single scene, the author strongly characterizes Rin and hints at a point of social criticism that he reinforces later on. The reader and Aoki first meet Rin as a cheerful and playful, though somewhat naughty girl, but very quickly, this scene juxtaposes this image with that of a child who is no longer a child. Her cruelty toward her previous teacher, her exposing herself, and her awareness of how society would interpret the scene all present an image of a girl all too aware of reality, no matter how society may want to imagine girls: as pure and innocent. Neither is her reaction childish: she doesn't blackmail Aoki because she's afraid of getting into trouble, but rather, as is revealed later, to keep Aoki from knowing that her parents are divorced and her mother dead. Rin wants Aoki's love rather than his pity.
As much as I would like to analyze Kodomo no Jikan in full, I simply don't have the time to piece together the countless meaningful, interconnected shards scattered throughout, and I did not take notes either, which is vital to writing analyses. Regardless, I can assure you that Kodomo no Jikan is a worthy read/watch. Pay attention to how each character is presented, especially Rin and Aoki, how their character and relationship changes throughout, and periodically ask yourself, "What is this saying about society?" I guarantee that you will find more than you expected.