During World War II, Jojo Betzler, a member of the Hitler Youth, wants to become an exemplary Nazi. He and his best friend, Yorki, go away to a training camp, led by Klezendorf, a buffoonish closeted gay Nazi, in the woods. Along the way, Jojo is accompanied by his imaginary friend—Adolf Hitler himself.
While at the training camp, Jojo gets bullied for not being able to kill a rabbit, which leads to his nickname, "Jojo Rabbit." Trying to prove himself to his fellow soldiers, Jojo throws a grenade into the forest, but it bounces off a tree and explodes a few feet away from him. He is sent to the hospital and endures scars on his face and an injury to his leg that leaves him with a limp. Back at home, his mother, Rosie, asks Klezendorf to accept Jojo into the Hitler Youth and help him feel like he belongs.
Soon after, Jojo learns that his mother is not such an avid supporter of the Reich when he finds a Jewish girl—Elsa, who used to be one of his late sister's classmates—hiding in the attic. He wants to report her to the Germans, but Elsa tells him that if he does he and his mother will be killed. Unable to turn her in, he insists that she reveal Jewish secrets in return for his silence. In the course of his questioning, Jojo learns about Elsa's life before the war, and that she has a fiancé named Nathan who is fighting in the resistance. Their friendship deepens, but they do not reveal to Rosie that Jojo knows about Elsa.
One day, while Jojo is collecting scrap metal in town for the war effort, he sees his mother leaving a "free Germany" message on a bench. At this point, he realizes she is working for the resistance, but does not confront her about it. Soon after, the Gestapo come to the house and search the house for evidence that Jojo and his mother are aligned with the resistance. Elsa presents herself to the Gestapo as Jojo's sister Inge and manages to fool them, but becomes certain the Gestapo will come back for her. They decide to tell Rosie everything that's happened and ask for her help, but the Gestapo have already executed her.
Jojo and Elsa wait out the end of the war in the house, and Jojo eventually emerges to find that the Allies have won and Hitler committed suicide. He gets rounded up with the other Nazis, but Klezendorf saves his life by pretending that he is a Jew. Jojo runs home and lies to Elsa, telling her that the Germans won. He tells her he loves her, and she says she loves him too, but as a brother. After they emerge out into the empty streets, Elsa and Jojo dance.
