The book starts by introducing young Bruno. He is very upset because his maid is packing all of his things and he doesn't understand why she would be touching all of his stuff. It turns out that his father is a German officer during World War II and his job is requiring a move from Berlin to Auschwitz (in Poland.)
In addition to the general Nazi vs. the Jewish conflict, there is also a conflict between Bruno and his parents. They don't fully realize how severe the conflict is (Bruno not liking his new home and lack of friends), but it leads to his escape into the camp.
Bruno goes against his mother's wishes and "explores" beyond the fenced backyard. He meets and befriends Shmuel and he begins to visit him daily. He sneaks food to him as well.
Bruno changes into a set of striped pajamas and crawls under the fence to the prisoner side. He leaves his clothes and boots behind. The two boys go to look around the prison grounds for Shmuel's father, who has gone missing.
Bruno and Shmuel get locked inside the prison.
Both Bruno and Shmuel are murdered in the gas chamber. This is never discovered by his parents, but it leads both into a world of despair and pain.