Johannes Betzler, called Jojo, ist a Hitler youth during the last months of World War II. Always at his side is his imaginary friend, Adolf Hitler, as well as his real friend Yorki.
During a training camp led by Captain Klenzendorf, Jojo refuses to kill a rabbit, earning him his nickname Jojo Rabbit. Determined to prove his bravery, he gives it his all during a grenade throwing exercise, but the grenade bounces off a tree and injures Jojo. He survives, but has to stay home for a while.
Here he meets the jewish girl Elsa Korr, who was hidden by Jojos parents in the attic. Torn between his nazi-ideology and his unwillingness to kill, a relationship develops between the two, which leads Jojo to question his beliefs.
During a search by the Gestapo Elsa poses as Jojos sister Inge. Captain Klenzendorf, who is also there, checks her identity. Despite making a mistake with the birth date, Klenzendorf doesn't call her out.
As the allies close in on Berlin, Jojo flees, just to be captured by soviet troops the next day and is brought to a backyard with other prisoners, among them Captain Klenzendorf. Klenzendorf calls Jojo a jew, which leads to Jojo being released.
He hurries home to Elsa and confesses his love, though Elsa sees him more than a brother. The imaginary Hitler is thrown out of a window.