Bruno's family has moved to a new place (which we find out is the Auschwitz concentration camp, where his father is Nazi official who oversees the running of the place). Bruno is lonely and bored in his new home. One day he comes across a small, skinny boy wearing pajamas (which are actually the uniform for all the Jews who are imprisoned in the camp). Bruno and the boy, Shmuel, talk and discover that they share a birthday. Then they part ways, agreeing to meet again. The friends continue to meet and become closer. One day Bruno enters the kitchen at his house. He finds Shmuel in the kitchen, working. Bruno has noticed that his friend is skinnier than when they first met, so he offers him food. Lieutenant Kotler, a man who works with Bruno's father, catches Shmuel with the food and becomes angry. Cowardice takes over Bruno, and he denies knowing Shmuel. Bruno does feel conviction and later apologizes.
Bruno finds out that his mother is taking him and his sister to Berlin soon. He decides to cross the fence and dress in the same uniform that Shmuel wears. They spend time together and look for Shmuel's father, who is missing. Soon they are rounded up by soldiers and led into a room. The door is closed and the boys hold hands. It is a gas chamber and the two boys are killed.
At first, Bruno wants Shmuel to be his friend because he is bored. He does not value their friendship much, as we see when Bruno denies him in front of Kotler. Later, Bruno comes to care more deeply for his friend. In the end, they comfort each other before they die.