In the waning days of World War II, a young German boy named Jojo Betzler lives with his mother Rosie. He is a fervent member of the Hitler Youth, complete with an imaginary friend who is a buffoonish version of Adolf Hitler himself. Jojo's blind nationalism is put to the test during a training camp for young Nazis, where an accident leaves him disfigured and his military dreams dashed. Ashamed of his injuries and demoralized, he finds solace in his patriotic zeal and the camaraderie of his imaginary advisor, while his loving and protective mother tries to shield him from the harsh realities of the war.

While exploring his home, Jojo discovers a Jewish girl named Elsa hiding in a secret compartment in his deceased sister's bedroom. Panicked and indoctrinated with anti-Semitic propaganda, Jojo is torn between his belief in Nazi doctrine and his inherent curiosity and humanity. Over time, as he covertly interrogates Elsa to learn about his supposed enemy, Jojo begins to question his beliefs. His interactions with Elsa reveal the dichotomy of war to him, pitting his ingrained ideology against the growing realization of the grim world around him and the absurdity of his prejudices.