Bruno, a nine-year-old boy living in Berlin, Germany in 1943, comes home one day to find his family’s maid, Maria, packing all of his things away in boxes. Bruno’s Mother explains that the family is moving away due to the demands of his father’s new job. “The Fury,” as Bruno calls Adolf Hitler, had come to dinner at Bruno’s home the previous week, and has promoted Bruno’s Father. Father is a Commandant in the German army. He is a stern and imposing figure, but still expresses his care for his children. Bruno is unhappy to be leaving his best friends, grandparents, and the hustle and bustle of Berlin, but is presented with no other choice than to go with his family. Before they go, Father gets into a fight with Bruno’s Grandmother, a former singing star, at their Christmas celebration. Grandmother is furious that Father would accept his new job from the Fury, but Father counters that it is a great honor for himself and for the Fatherland.
The family packs up all of their belongings and soon head out on a train to reach their new home. The new house on a hill is the only house in a very desolate area. Bruno is sad to be away from Berlin, and bored to have only his twelve-year-old sister Gretel, whom he does not get along with, for company. Their maid Maria and butler Lars staff the house, but there are also new waiters that Bruno has not met before. One of them, Pavel, is an old, stooped man who cleans up Bruno’s cut knee one day when he falls from a tire swing. Pavel tells Bruno that he has been a doctor in a past life, and Bruno is confused as to why a doctor would be working as a waiter in his house. Bruno comes to learn that Pavel lives on the other side of a fence that runs near their house. On the other side of the fence, as Bruno can see from his bedroom window, are thousands of people living in a sandy, fenced-in camp, all wearing “striped pajamas.” Bruno cannot properly pronounce the name of their new home, but calls it “Out-With” (Auschwitz).
As Bruno settles into life at Out-With, he comes to dislike Lieutenant Kotler, a soldier who hangs around their house and whom Gretel has a crush on. Kotler is harsh and calls Bruno “little man.” Mother takes a liking to Lieutenant Kotler, though everyone is horrified when he beats Pavel one day for spilling a glass of wine. Bruno is given lessons in history by a tutor named Herr Liszt, who tells him that Bruno’s father and his family are at Out-With in order to correct the “great wrongs” that have been done to him. Gretel becomes very involved with history and politics, and takes to tracking the events of the news via pushpins in maps on her wall.
Bruno misses the exploring he so enjoyed in Berlin, and one day he walks along the length of the fence, despite the fact that he has been forbidden to do so. He meets a boy who lives on the other side of the fence named Shmuel. Shmuel wears the striped pajamas that Bruno has seen from his window, and he is extraordinarily thin. The two boys strike up a friendship, and Bruno begins to visit Shmuel nearly every day. Shmuel tells him how he was taken by soldiers from his home in Cracow, Poland, to the camp, which Bruno comes to realize is also in Poland. Bruno struggles to understand exactly what life is like on Shmuel’s side of the fence, but complies when Shmuel asks him to bring him food.
Bruno begins to like life at Out-With a lot more as his friendship with Shmuel develops. One day he is shocked to find Shmuel inside his house—Lieutenant Kotler had brought him there to shine the family’s tiny glasses, a job for someone with small hands. Bruno nonchalantly gives his friend a piece of leftover chicken. Kotler catches them, and demands to know if Bruno is friends with Shmuel. Terrified, Bruno denies knowing the boy, and Kotler later beats Shmuel. Kotler is later transferred away from Out-With—due to the fact that he reveals to Father that his own father fled from Germany to Switzerland in 1938, at the onset of World War II.
Eventually, Mother convinces Father to move the family back to Berlin. He consents, though he himself will remain at Out-With due to obligations to his job and the Fury. Bruno is saddened to leave Shmuel behind. When he goes to say goodbye, the boys agree that Bruno will dress up in striped pajamas the following day, in order to explore Shmuel’s side of the camp and to help Shmuel search for his father, whom he has not seen for several days.
The next day, Bruno dresses up in pajamas Shmuel has brought him, and climbs under the fence. Inside he finds people sick and thin, with soldiers yelling at them. Scared, he wants to leave, but Shmuel asks him to help him find his father. Though they find nothing, the soldiers round up prisoners for a march before Bruno can sneak back under the fence. Scared, the two boys comply, and end up in a dark room together. They hold hands as the soldiers shut the doors, and everything goes dark.
Bruno is never heard from again. His mother and sister eventually return to Berlin, and his father becomes hated by the soldiers for his merciless orders. Bruno’s clothes and boots are found where he left them outside the fence when he changed, and one day Bruno’s father pieces together what must have happened to his son. He collapses from the weight of his realization, and months later, different soldiers arrive at the camp. Father complies with all of their demands, as he no longer cares what happens to him after realizing his son’s grim fate.