NOTE: This spoiler was sent in by Emily.
The show starts out with Bruno running through the streets with three of his friends, mimicking airplanes. When they get to Bruno's house, he is confused by the tons of flowers being brought into it. He asks his mother what is going on and she informs Bruno that his father Ralf got a promotion and that he has something to tell him and his older sister Gretel. It turns out that the promotion will cause them to have to move to the country. Bruno is not pleased at this, as he will no longer be able to play with his friends. The incoming flowers turn out to be for a party in honor of the promotion, which is attended by many soldiers. Ralf's parents are also there and while his father is pleased, his mother turns out to be very anti-Hitler.
The next morning Bruno is allowed to play with his friends one last time before the family travels to their new home, which look more like a stone fortress then the fancy house they left behind. There is a constant company of soldiers in and around the house, which seems to make Bruno uncomfortable.
From his new room, Bruno can see what he believes to be a farm, with the workers wearing striped pajamas. He questions his mother about this just as a weary looking man delivers some vegetables. From under the bottom of his trousers, striped pants peek are seen at which Bruno comments "I told you they were strange." His mother, Elsa, confronts Ralf and says, "You said that it would be miles away."
After two weeks of playing checkers with himself and exploring a very small front yard, Bruno is terribly bored as he has been forbidden to explore the back of the house. Bruno approaches one of the soldiers, Lt. Kotler, who is often around the house while he is washing the car with Gretel who is obviously flirting, and asks if he knows where a tire is, as he wants to make a swing. Kotler shouts at the weary man who does quiet a bit of work around the house and angrily tells him to go to the back hut to get a tire for the boy. Bruno is very startled at the Lts tone of voice.
Bruno follows the man into the forbidden backyard and they find a tire. He also notices a window in the hut leading to the outside woods. After his swing is created, he is swinging when he suddenly notices smoke in the distance and a funny smell. He is so focused on the smoke that he falls of the swing and scrapes his knee. The weary man takes him into the kitchen and bandages his knee all the while Bruno is exclaiming he should go the hospital, as it could be worse then it looks. The man, Pavel, assures him that it is fine and Bruno says "How should you know, your not a doctor." Pavel tells him that yes he was a doctor before he came to the "farm". Bruno does not understand why he would give up being a doctor to peel potatoes.
Later in the week, Bruno sneaks back to the shed and opens the window and gains the freedom from boredom he has been waiting for. He runs quite a way until he sees the fence from the farm. Through the fence he sees a boy who he goes up to talk to. Bruno is curious why they wear pajamas all day and the boy, Shmuel, tells him it is because the soldiers took their other clothes away. They discover they are both eight and that neither really have friends. A whistle blows and Shmeul darts up to get a wheelbarrow and they joke about each other’s names and hope to meet again.
They meet together often, Bruno usually bringing snacks and Shmeul hastily eating everything he is given. Bruno continuously asks questions about life on the other side. Meanwhile, a new tutor is teaching Bruno and Gretel the history of the fatherland and about the evil Jew, with Gretel buying into it all wholeheartedly.
One day, the mother comes home from shopping and smells the stench from the smoke at which Lt. Kotler comments, "They always smell worse when they burn." Elsa is utterly horrified, as she had no idea that that was what was really going on. She breaks down screaming at Ralf that what he is doing is not fighting the war.
The discovery came at a pretty bad time, as Grandpa is almost here to visit. During dinner, it is extremely tense, and during halfhearted small talk Lt. Kotler accidentally lets slip that his father had left for Switzerland before the war, which in Ralf's eyes, is a traitor to the state, which leaves Kotler in hot water as he is supposed to report "treason" to the authorities. Ralf angrily calls for more wine and Pavel, who seems to be very sad and out of it, spills Kotler's cup on the table. Kotler viciously drags him out and beats him in the kitchen. Elsa and the children are mortified and Ralf just keeps eating as if nothing happened, Grandpa doesn't seem to mind much either. Pavel never returns.
Instead, the next day Bruno is ecstatic to find Shmuel in his house cleaning glasses. Bruno informs Shmuel that they are supposed to be enemies, but instead offers him a pastry. They talk about something until a very scary looking Kotler comes in and gets very angry with Shmeul and asks him how he got the pastry. Shmeul tells him that Bruno gave it to him, but Bruno, who is as terrified as Shmeul of Kotler claims that he did not know him and he walked in on him eating it. Kotler tells Shmeul that they will have a chat about what happened and escorts Bruno out who promptly runs upstairs and cries. He does not see Shmeul for days, as he is not at his usual spot by the fence.
Meanwhile, his parents are constantly fighting and Bruno realizing, thanks to his sister, that the farm is a camp for Jews and Bruno states it's terrible, and his sister agrees but says "Only for them." He begins to doubt that his father is a good man.
Kotler is also sent to "the front." Grandma also dies in the bombing of Berlin. Bruno also sees a propaganda film his father made showing the camps to be more like displaced persons camps with cafes and gardens and other wonderful things for the Jews to do. Bruno seems relived to see that.
Finally, much to Bruno's relief, he finds Shmeul sitting by the fence after many days absence, although worse for the wear with a black eye. He apologizes and hopes that they can still be friends. Shmeul quietly agrees and they shake hands and continue to talk and play checkers.
One day, Bruno's father announces that they will sending the children somewhere else for the duration of the war and is surprised by Bruno's unwillingness to leave. On that same day Shmeul is very upset, as he can't find his father. Wanting to make up for his betrayal at the house Bruno says he will come help him tomorrow. Shmeul will bring an extra pair of pajamas and Bruno will bring a shovel.
The next day they meet and begin their "secret mission" by digging a hole big enough for Bruno to get under the fence and change. This done, they begin looking in different huts.
Meanwhile Bruno is discovered to be missing. The boys wander into one hut where it is packed with still silent men and buzzing flies. All of a sudden guards burst in and herd everyone out, down a path. It is unclear whether the guards know that the boys are in the group as they are squished into the middle barely able to keep upright. They stumble over a man in the pathway who is shot in the head after they pass. They are all led down some stairs into what looks like a kind of locker room. Both boys are clueless to what’s going on while some of the older men seem to know. Bruno is relived to discover that they are just going to take a shower.
Meanwhile, Bruno's parents and many guards are combing the woods for Bruno.
The group is herded into a crowded room and is locked in. The two boys grab hands as someone in a gas mask pours powder down on them as the lights go out.
Bruno's clothes are discovered near the fence and his mother gets hysterical and by the time the father looks though some huts and realizes where Bruno probably was, the door leading to the gas chamber is deathly silent.