The film opens in 1482 Paris with Clopin, a gypsy puppeteer, telling a group of children the story of the Hunchback of Notre Dame. The story begins as three gypsies sneak illegally into Paris but are ambushed by a squadron of soldiers working for Judge Claude Frollo, the Minister of Justice and de facto ruler of Paris. A gypsy woman attempts to flee with her baby, but Frollo catches and kills her just outside Notre Dame, intending to kill her deformed baby, but the Archdeacon appears and accuses him of murdering an innocent woman. To atone for his sin, Frollo agrees to raise the deformed child in the Cathedral as his son, naming him Quasimodo.

Twenty years later, Quasimodo has developed into a kind yet isolated young man with three gargoyles as his only company, constantly told by Frollo that he is a monster who would be rejected by the uncaring outside world. Despite these warnings, Quasimodo sneaks out of the Cathedral to attend the Feast of Fools, where he is crowned King of Fools but immediately humiliated by the crowd. Frollo, in the audience, refuses to help Quasimodo, and the crowd only stops when a kind gypsy, Esmeralda, frees Quasimodo from his restraints and openly defies Frollo. Frollo orders her arrested, but she escapes by means of magic. Frollo scolds Quasimodo and sends him back inside the Cathedral.

Esmeralda follows Quasimodo to find him, but is herself followed by Phoebus, Frollo's Captain of the Guard. Phoebus, who himself does not approve of Frollo's methods, refuses to arrest her inside the Cathedral, and Frollo finally leaves when the Archdeacon orders him out, but not before warning Esmeralda that he will capture her the minute she leaves the Cathedral. Esmeralda finds Quasimodo in the bell tower and befriends him. As gratitude for helping him in the crowd, Quasimodo helps Esmeralda escape Notre Dame. In return, she leaves him with a map to the gypsy hideout, the Court of Miracles, should he ever choose to leave Notre Dame again. Frollo himself begins to realize his lustful feelings for Esmeralda and wishes to be free of them to escape Eternal Damnation. He soon learns of Esmeralda's escape, and orders a city-wide manhunt for her, burning down houses in his path. Realizing Frollo is losing his mind, Phoebus defies Frollo, who orders him shot and executed. Phoebus falls into the river, but is rescued by Esmeralda, who takes him to Quasimodo for refuge.

Frollo soon returns to the Cathedral, forcing Quasimodo to hide Phoebus. Knowing Quasimodo helped Esmeralda escape, Frollo bluffs that he knows where the Court of Miracles is and that he intends to attack it at dawn with a battalion. After he leaves, Phoebus requests Quasimodo's help in finding the Court before Frollo. Using the map Esmeralda left, they eventually find the Court and are almost hanged by the gypsies as spies, but are saved when Esmeralda intervenes and clears up the misunderstanding. However, Frollo's army appears and captures them all, with Frollo revealing that he followed Quasimodo.

Frollo orders Esmeralda burned at the stake after she refuses his proposal of her becoming his mistress. Quasimodo, tied up in the bell tower, initially refuses to help, but seeing Esmeralda in pain causes him to give in to his anger and rescue her. Phoebus ignites a mutiny and a battle ensues in the street between the citizenry and Frollo's men. Quasimodo places Esmeralda's unconscious body on a bed and pours a cauldron of molten copper onto the streets to ensure nobody gets inside. Frollo, however, manages to break in and force his way past the Archdeacon. Quasimodo, believing Esmeralda to be dead, breaks down beside her body as Frollo comes into the room to kill him with a dagger. Quasimodo, in his fury, almost kills Frollo but stops when Esmeralda wakes up. Frollo chases them to the balconies where they fight. The battle ends with both Frollo and Quasimodo falling off the balcony. While Frollo falls to his death, Quasimodo is caught by Phoebus on a lower floor, and the three friends reunite.

As the citizens celebrate their victory over Frollo, Quasimodo reluctantly emerges from the Cathedral to face the populace again, only this time, he is hailed as a hero.