This book is about a nine-year-old boy named Bruno, who liked nothing more than going to school or playing around with his friends. But because of his father's job, he is forced to move from his home in Berlin to Poland. In his new house at Out-With from his bedroom window, Bruno spots a fence behind which he sees people in striped clothing. (Those people were Jews, and they were put in the Nazi concentration camp). One day, his parents come to an agreement that both Bruno and Gretel, his sister, need a tutor for their education, so they hire Herr Liszt. To Bruno's opinion, Herr Liszt was the most boring teacher anyone could ever have because he only taught social studies, but Bruno perfered reading and arts, which were his favourites. One afternoon, Bruno goes exploring and at one point, stops at the tall fence he once saw from his bedroom window. He then meets a Jewish boy sitting on the ground on the other side of the fence, name Shmuel, a name Bruno has never heard of before. Shmuel soon becomes Bruno's friend, even though they are separated by the tall fence of the camp. This then leads Bruno, to daily visit Shmuel every afternoon at the fence to talk. Bruno is told by Gretel that the people in the striped pyjamas on the other side of the fence are Jews and that he and his family are "the opposite".
The story slowly ends with Bruno about to go back to Berlin with his mother and sister on the orders of his father. As a final adventure, he agrees with Shmuel to dress in a set of striped pyjamas and goes in under the fence to help Shmuel find his father, who went missing in the camp. Sadly, the boys were unable to find him, and just as it started to rain and get dark, Bruno decides he would like to go home, but they are rounded up in a crowd of people by the nazi guards who start them on a march. Neither boy knows where this march will lead. However, they are soon crowded into a gas chamber, which Bruno assumes is a place to keep them dry from the rain until it stops. The author leaves the story with Bruno preoccupied, yet unafraid, in the dark holding hands with Shmuel.
In an epilogue, Bruno's family spend several months at their home trying to find Bruno, before his mother and Gretel return to Berlin, only to discover he is not there as they had expected. A year afterwards, his father returns to the spot that the soldiers found Bruno's clothes (the same spot Bruno spent the last year of his life) and, after a brief inspection, discovers that the fence is not properly attached at the base and can form a gap big enough for a boy of Bruno's size to fit through. Using this information, his father eventually pieces together that they have gassed Bruno to death. Several months later, the Red Army arrives to release the camp and orders Bruno's father to go with them. He goes without complaint, because "he didn't really mind what they did to him anymore".
