Au Revoir, Les Enfants contains themes similar to other Holocaust films, though they are less directed and explicit.

One theme is that understanding is important. Julien becomes friends with Jean, even though all the other boys make fun of him. Though Julien goes to a fiercely Catholic school he does not care at all that Jean is actually Jewish and is only surprised when he finds out Jean's secrets.

Another theme is the fragile power of innocence and its destruction. Julien is completely naive of the outside world. At one point in the film, he asks his brother what a Jew is, to which his Francois replies, "Someone who doesn't eat pork." It is through Julien's innocence that he is able to not care about Jean being Jewish, even though that is one of the main concerns of the war and Hitler's Germany. Ultimately this fragile innocence is destroyed when Jean and the other Jewish boys along with the headmaster Pere Jean are taken away.

Another theme is the absurdity of the war. When Julien asks Francois why everyone hates the Jews, Francois replies that "they're smarter than us, and they crucified Christ" to which Julien replies, "No they didn't, the Romans did". Through this small exchange the audience can see the absurdity and groundlessness of the whole war. Also, when the Quentin family is out eating, a French collaborator tries to get an elderly rich Jew to leave, even though he has eaten at that restaurant every day. People who were once respected are now hated and in this light the hatred seems almost silly.

Louis Malle does not give a concrete message to the audience. Most of the film is frivolous, with the story revolving around the daily lives of the children at the boarding school. Only the climax, where the children are arrested, seems to have any "weight". Though one obviously feels bad for the Jewish children and the headmaster who tried to save them, the audience can also see Joseph's point that one has to do what one must to survive (as he says, "Stop being so pious...there's a war going on"). Thus Malle leaves the audience in a grey area. He makes an eloquent statement at the end however when the adult Julien comments that he will never forget the events of that day no matter how long he lives.