In the later stages of World War II, ten-year-old Johannes “Jojo” Betzler joins the Deutsches Jungvolk. Jojo is an innocent boy but heavily indoctrinated with the Nazi ideals (manifested in his imaginary friend, Adolf, a supportive and buffoonish version of Adolf Hitler). On the day of his first Hitler Youth training camp run by Captain Klezendorf, he is given the derisive nickname “Jojo Rabbit” by the other children after refusing to kill a rabbit to prove his killer instinct.
Pepped up by Adolf, he returns to prove his bravery, stealing a Stielhandgranate and throwing it without supervision. The grenade explodes at his feet, leaving him scarred and limping. Jojo‘s mother Rosie coerces Klenzendorf into ensuring that Jojo is included and given responsibilities. Jojo is given small tasks such as spreading propaganda leaflets throughout the town, and collecting scrap for the war effort.
Alone at home one day, Jojo discovers Elsa Korr, a teenage Jewish girl and his late sister’s former classmate, hiding upstairs. Jojo is both terrified and aggressive towards Elsa, who easily outwits and overpowers the young boy’s attempts at guile and aggression.
The two are left in a stalemate as the revelation that Rosie is hiding Elsa would lead to Rosie’s and Jojo’s executions, and neither is willing to tell Rosie that they know for fear of what would happen next. Jojo continues to speak to Elsa, doing his best to uncover her “Jew secrets” so he can write a book about Jews for Klenzendorf. Elsa is both saddened and amused by the doctrine that Jojo believes. When she tells Jojo about her fiancé Nathan, Jojo forges a letter from Nathan claiming to have found someone else. When he sees her hurt by this, he quickly puts together a retraction.
Jojo begins acting out with his mother, angry at her seeming lack of patriotism. Rosie opposes the war and the Nazi doctrine, openly mourns the public hangings of those who resist the Nazis, and she espouses her belief that positivity and optimism are the best ways to be free of oppression. Rosie also tells Elsa that Jojo is still innocent and laments the doctrine that he believes, which makes it impossible for her to reveal Elsa to him. Meanwhile, Jojo, who is warming up to Elsa, argues with an increasingly hostile Adolf about his patriotism. Jojo spots his mother leaving a “free Germany” message in town.
Jojo and Elsa are alone in the house when the Gestapo stops by for a surprise inspection with Klenzendorf in tow. The Gestapo is suspicious when Elsa poses as Jojo’s late sister and produces Inge’s papers. Klenzendorf inspects them and quizzes Elsa on her birthday, confirming its authenticity. After the Gestapo leave, a shaken Elsa reveals that she got the date wrong and that Klenzendorf had covered for her. Elsa is convinced that the Gestapo are aware of the deception. Later on, Jojo finds Rosie hanged in the public square. He returns home and tries to stab Elsa, but breaks down in tears.
With the Allies closing in, the civilian population (including the Hitler Youth) are armed to defend the city. Jojo runs into his friend Yorki, who tells him Hitler has committed suicide. Despondent, Jojo hides until the battle is won, with the Americans and Soviets occupying the city. As he wanders the city, he is seized by the Soviets who imprison him, and Klenzendorf. A wounded Klenzendorf tells Jojo to look after his sister, then tears off Jojo’s Hitler Youth coat and denounces him as a Jew. The Soviets expel Jojo as they drag Klenzendorf towards the firing squad.
Jojo runs home and, to stop Elsa from leaving, tells her Germany won the war.