The innocent and unsuspecting son of a Nazi officer, nine-year-old Bruno is a German boy who finds himself unexpectedly uprooted from a civilized and comfortable life in an upper-class section of Berlin where he has friends and grandparents.
After arriving at Auschwitz, Bruno is surprised by the isolation of the place and the inferiority of their new house when compared to the one in Berlin. He finds it "the loneliest place in the world," and he cannot find anything “to laugh at and nothing to be happy about.” There are no other children with whom he can play; there is no park, no interesting buildings and no museums to visit. He does not like the young lieutenant who comes to his father's office.
After several weeks at what Bruno calls "Out-With," Bruno makes an effort to amuse himself since he has no friends. When he notices a tree with a sturdy lower branch, Bruno goes outside after locating rope in the basement. He approaches Lieutenant Kotler, who talks with Bruno's sister, Gretel, and asks the young officer if there are any tires that he can use for a swing. Kotler harshly calls Pavel, an older man who prepares the evening meals for the family. Later, Bruno falls out of his swing and injures himself. Pavel comes to Burno's rescue by carrying the boy inside where he administers to the gash in his leg. Afterwards, Pavel explains to a worried Bruno that he used to be a physician, and he knows how to care for wounds. When Bruno's mother returns, the boy tells his mother what happened. As he heads to his room, Bruno wonders why his mother instructs Pavel that she will tell the Commandant that it was she who tended to the wound on Bruno.
One day, Bruno decides to explore the large, desolate area that is fenced and tries to discover what it is that makes the people in striped "pajamas" different from the other men who seem to herd them around the area. When he reaches the fence, Bruno walks along the perimeter, but he sees no one and no place where he can enter. Finally, he encounters a small boy with "an enormous pair of sad eyes” who sits on the ground. Bruno talks with this boy named Shmuel, who is also nine and has the same birthday as Bruno. As they talk, Bruno naively asks Shmuel why so many people are inside the fence and what they are doing.
One evening Bruno discovers Shmuel in his kitchen. Shmuel tells Bruno that he was brought in to clean inside the glasses because he has small fingers. It is then that Bruno notices that Shmuel’s fingers look like “dying twigs” and he finally begins to think that whatever goes on at Out-With is “a very bad idea.” When he pulls out some pieces of chicken from the refrigerator, Bruno notices the intense watchfulness of Shmuel, so he offers the thin boy the meat. Unfortunately, Shmuel is observed eating the chicken by Kotler. When he is interrogated, Shmuel tells the lieutenant that Bruno gave it to him, but, out of fear of Kotler, Bruno denies that he has done so.
Ashamed of his behavior, Bruno apologizes to Shmuel at the fence when he next sees the frail boy. Shmuel tells him it is "all right," but he has bruises all over his face. Bruno feels terrible. It is not long before Bruno learns that he, along with his mother and Gretel, is to return to Berlin. When he next talks with Shmuel, Bruno learns that Shmuel cannot locate his father. Wishing to be together, Bruno and Shmuel come up with a plan. Shmuel finds an extra pair of striped "pajamas," and Bruno climbs into them. He crawls under the fence, and they search for Shmuel's missing father. Bruno begins to feel a strange presentiment that something is wrong—and he wants to go back—but suddenly there is a whistle sound. The boys are then pushed into the center of a mob, and they are all moved into a stifling room. Bruno takes Shmuel's hand, telling him that he is Shmuel's "best friend for life." They die together in a gas chamber.