In a world populated by anthropomorphic mammals, a rabbit from rural Bunnyburrow, Judy Hopps, fulfills her childhood dream of becoming the first rabbit police officer in Zootopia, an urban utopia. Despite being the police academy valedictorian, Judy is relegated to parking duty by Chief Bogo, who doubts her potential. On her first day, she is hustled by Nick Wilde and Finnick, a con artist duo.
The next day, Judy abandons duty to arrest Duke Weaselton, a thief who has stolen plant bulbs. Bogo reprimands her, but a female otter named Mrs. Otterton enters Bogo's office pleading for someone to find her missing husband Emmitt, one of a string of disappearances of predators, a minority group. Judy volunteers, causing Bogo to fire her for insubordination. However, when Assistant Mayor Bellwether praises the assignment and informs Mayor Leodore Lionheart that Judy is taking the case, Bogo gives her two days to find Otterton on the condition that she must resign if she fails.
Judy discovers that Nick was the last one to see Otterton. She blackmails him into assisting her by covertly recording his confession to tax evasion. They track Otterton to a limousine owned by crime boss Mr. Big, who reveals that his florist Otterton went "savage" – reverted to a feral state – and attacked his chauffeur Manchas. At his home, Manchas mentions that Otterton had been yelling about "night howlers." Suddenly, Manchas himself goes savage and chases the pair. Judy saves Nick by trapping Manchas and calls the ZPD for help; when Bogo and other police arrive, however, Manchas has vanished. Bogo demands Judy's resignation, but she is saved by Nick, who reminds Bogo that she still has ten hours to solve the case. As they leave, Nick reveals to Judy that he was bullied as a child for being a fox; deciding there was no use in fighting prejudiced ideas about fox behaviour, he became a con artist.
Bellwether gives Judy and Nick access to the city's traffic camera system. They discover Manchas was captured by wolves, which Judy surmises are the "night howlers". They find Otterton and the other missing predators imprisoned in a secret asylum where Lionheart has been keeping them hidden from the public and trying to determine the cause of their strange behavior. Lionheart is arrested, Bellwether becomes the new mayor, and Judy is praised for solving the case. Judy asks Nick to join the ZPD and become her partner, but when she upsets him by suggesting a biological cause for the recent predator behavior at a press conference, he leaves angrily. Guilt-ridden, Judy quits her job amid a wave of protests against predators.
Back in Bunnyburrow, Judy learns from her parents and reformed childhood bully, fox Gideon Grey, that "night howlers" are toxic flowers that have severe psychotropic effects on mammals. After Judy returns to Zootopia and reconciles with Nick, they find Weaselton and discover that the bulbs he was stealing were night howlers intended for a ram named Doug. They find Doug in a lab hidden in the subway tunnels, creating a night howler serum which he has been injecting into predators via a dart gun.
Before they can go to the ZPD, Bellwether steals the evidence, revealing herself as the mastermind behind a prey-supremacist conspiracy. Judy and Nick are trapped in a pit by Bellwether's henchrams after Nick refuses to abandon Judy when she is injured. Bellwether calls the police, intending to use the serum to make Nick kill Judy, but Nick had replaced the dart gun's serum pellets with blueberries and Judy has recorded Bellwether's confession. The police arrive and arrest Bellwether. Lionheart denies knowledge of Bellwether's plot, but asserts that he imprisoned the savage predators for the "right reasons." The savage predators are cured by an antidote. Judy rejoins the ZPD, Nick becomes her partner and the first fox police officer.