The movie 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 soldier-like thugs 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, thinking the woman is carrying stolen goods, catches and kills her just outside Notre Dame, intending to kill her deformed baby (Frollo says to the Archdeacon that the baby is "an unholy demon" and that he is "sending it back to hell where it belongs"), but the Archdeaconappears and accuses him of murdering an innocent woman. Frollo denies that he is in the wrong saying his conscience is clear, but the Archdeacon declares he can lie to himself all he wants, but he cannot hide his crime from heaven ('the eyes of Notre Dame', the statues of the saints outside the cathedral). Fearing for his soul and to atone for his sin, Frollo reluctantly agrees to raise the deformed child in the Cathedral's bell tower as his son, naming him Quasimodo. He notes that someday the child may have use for him.
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 when Frollo's thugs start a riot. Frollo, in the audience, refuses to help Quasimodo, and the crowd only stops when a kind and beautiful gypsy Esmeralda frees Quasimodo from his restraints and openly defies Frollo. She then throws the crown at Frollo, deeming him to be the biggest fool. The judge immediately orders her arrested, but she escapes by means of illusions, which Frollo refers to as "witchcraft." Frollo confronts Quasimodo and sends him back inside the Cathedral.
Esmeralda follows Quasimodo to find him, but she herself is 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, saying that she has claimed 'Sanctuary' and thus cannot be arrested as long as she remains in Notre Dame. Frollo finally leaves when the Archdeacon intervenes, but not before warning Esmeralda that his men will capture her the moment she attempts to escape 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 instigates a city-wide manhunt for her, which involves burning down countless houses in his path.
Realizing that Frollo has lost his mind, Phoebus defies the judge by saving an innocent family, as Frollo orders him executed for treason, but is assisted in escape by Esmeralda. After being hit by an arrow, Phoebus falls into the Seine River and is left for dead by Frollo, but he is rescued by Esmeralda, who takes him to Quasimodo for refuge.
Frollo soon returns to the Cathedral, forcing Quasimodo to hide Phoebus. Discovering that Quasimodo helped Esmeralda escape, the judge 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, though reluctant he agrees to join. Using the map Esmeralda left, they find it and are almost hung by Clopin for being spies, but they are saved when Esmeralda intervenes and clears up the misunderstanding. Phoebus tries to get the court to retreat as Frollo plans to invade however, Frollo's army appears and captures them all, with the judge revealing that he followed Phoebus and Quasimodo.
Frollo then orders Esmeralda burned at the stake after she refuses his proposal of her becoming his mistress. Quasimodo, chained up in the bell tower, initially refuses to help under depression, but when he sees Esmeralda in pain, he gives into his anger and rescues her, bringing her to the cathedral and yelling "Sanctuary." As Frollo grabs a sword and orders his men to attack the cathedral, Phoebus ignites a rebellion among the people of Paris who have had enough of Frollo's tyranny and a battle ensues in the street between the citizenry and Frollo's thug army. 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 in tears beside her body as Frollo comes into the room to kill him with a dagger. Quasimodo, in his fury, disarms his former guardian and finally rejects all that Frollo had taught him. Esmeralda wakes up, alive, and Quasimodo grabs her and flees. The deranged judge chases them onto the balcony, where he attacks Quasimodo and Esmeralda with his sword. The battle ends with Frollo maniacally quoting the Bible and him and Quasimodo both falling from the balcony. After Frollo falls to his death, Quasimodo also falls but 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 and is finally accepted into society.