During the collapse of Nazi Germany in the city of Falkenheim,[a] ten-year-old Johannes "Jojo" Betzler joins the Deutsches Jungvolk, the junior section of the Hitler Youth (HJ). Heavily indoctrinated with Nazi ideals, he has an imaginary friend named Adolf, a buffoonish version of Adolf Hitler. The local HJ training camp is run by the conflicted Captain Klenzendorf. Though a fanatic, Jojo is nicknamed "Jojo Rabbit" after refusing to kill a rabbit to prove his worthiness. Pepped up by Adolf, he returns to prove himself, throwing a Stielhandgranate by himself that explodes at his feet. His mother Rosie insists to the now-demoted Klenzendorf that Jojo still be included, giving him small tasks like spreading propaganda leaflets.
Alone at home one day, Jojo discovers Elsa Korr, a teenage Jewish girl and his late sister Inge's former friend, hiding behind the walls of Inge's attic bedroom. Jojo is both terrified of and aggressive towards Elsa. The two are left at an impasse, as the revelation of Rosie's hiding of Elsa would lead to the execution of all three of them. Inspired by an offhand rant by Klenzendorf, Jojo continues to interact with her to uncover her "Jew secrets" and make a picture book titled Yoohoo Jew,[b] allowing people to easily recognize her kind. Despite this, he finds himself clashing with innocence, and slowly forming a friendship with her. Elsa is both saddened and amused by Jojo's radical beliefs, using surreal antisemitic canards to challenge his dogmatism. Jojo slowly becomes infatuated with the strong-willed and kind Elsa, frequently forging love letters from her fiancé Nathan, and begins questioning his beliefs, causing Adolf to scold him over his diminishing patriotism.
Gradually, Rosie is revealed to be part of the German resistance to Nazism, spreading anti-Nazi messages around town.[c] One day while she is out, the Gestapo come to investigate; Klenzendorf arrives and helps Jojo and Elsa deceive the Gestapo regarding Elsa's identity. Later, Jojo finds Rosie has been executed at a gallows in the public square. Devastated, he returns home and tries to stab Elsa before breaking down in tears. Elsa comforts him and also reveals that Jojo's lost father has been working against Hitler from abroad. Jojo's beliefs on Nazism quickly shift, as he sees the regime's inhumanity. With no money, he begins to scavenge food for them both from waste bins around the city.
Following Hitler's suicide, the Allies initiate an offensive on Falkenheim.[d] Weakened, the civilian population including the Jungvolk is pressed into combat service. Jojo hides until it ends with an Allied victory. As a Jungvolk, he is seized by Soviet soldiers alongside Klenzendorf, who tells him to look after Elsa, tears off his Jungvolk coat while calling him a Jew so the soldiers do not harm him. Klenzendorf is then executed by firing squad. Fearing that Elsa will leave him, Jojo tells her Germany won the war. Recognizing her despair, he forges a letter from Nathan, claiming that he and Jojo have figured out a way to smuggle her to Paris. Elsa confesses that Nathan died of tuberculosis the previous year. Jojo tells her he loves her, but she tells him she loves him as a brother. A disheveled Adolf angrily confronts Jojo for siding with Elsa, but Jojo kicks him out a window. Outside, Elsa sees American soldiers and realizes the truth, slapping Jojo in the face for lying. They then dance, now free.
