This offbeat stop-motion animated musical fantasy is set in an unspecified Victorian-era village somewhere in Europe, Victor Van Dort (Johnny Depp), the son of nouveau riche fish merchants, and Victoria Everglot (Emily Watson), the neglected daughter of hateful aristocrats, are preparing for their arranged marriage, which will raise the social class of Victor's parents and restore the wealth of Victoria's penniless family. Both have concerns about marrying someone they do not know, but upon meeting for the first time, they fall for each other.
After the shy Victor ruins the wedding rehearsal and is scolded by Pastor Galswells (Christopher Lee), he flees and practices his wedding vows in the nearby forest, placing the wedding ring on a nearby upturned tree root.
The root turns out to be the finger of a murdered woman in a tattered bridal gown, who rises from the grave claiming that she is now Victor's wife.
After fainting, Victor wakes up and finds out he was spirited away to the surprisingly festive Land of the Dead. The bewildered Victor learns the story of how Emily (Helena Bonham Carter), his new bride, was murdered years ago by an unknown criminal on the night of her secret elopement. Emily, as a wedding gift, reunites Victor with his long-dead dog, Scraps. Meanwhile, Victoria's parents hear that Victor has been seen in another woman's arms, and become suspicious.
Wanting to reunite with Victoria, Victor tricks Emily into taking him back to the Land of the Living by pretending he wants her to meet his parents. She agrees to this and takes him to see Elder Gutknecht (Michael Gough), the kindly ruler of the underworld, to send him and Emily temporarily to the Land of the Living.
Once back home, Victor asks Emily to wait in the forest while he rushes off to see Victoria and confess his wish to marry her as soon as possible, to which she gladly returns his feelings. Just as they are about to share a kiss, Emily soon arrives and sees the two of them together and, feeling betrayed and hurt, angrily drags Victor back to the Land of the Dead.
Victoria tells her parents that Victor has been forcibly wed to a dead woman, but they believe she has lost her mind and lock her up in her bedroom. She escapes her room by window and rushes to Galswells to find a way to help Victor, but fails. With Victor gone, Victoria's parents decide to marry her off to a presumably wealthy newcomer in town named Lord Barkis Bittern (Richard E. Grant), who appeared at the wedding rehearsal, against her will.
Emily is heartbroken by Victor's deception. Victor, however, apologizes for lying to her, and the two reconcile while playing the piano together. Shortly after, Victor's recently-deceased family coachman appears in the afterlife and informs Victor of Victoria's impending marriage to Barkis. In order for their marriage to become valid, Victor must repeat his vows in the Land of the Living and willingly drink the Wine of Ages, a poison - thus joining her in death.
Overhearing this, and fretting about having lost Victoria to another man, Victor agrees to die for Emily. All of the dead go "upstairs" to the Land of the Living to perform the wedding ceremony for Victor and Emily. Upon their arrival, the town erupts into a temporary panic until every living person recognizes each other's loved ones from the dead and they have a joyous reunion under the bizarre circumstances.
After a quarrel with Barkis (and realizing he was only after her supposed money), Victoria follows the procession of dead to the church. Emily notices Victoria and realizes that she is denying Victoria her chance at happiness the same way it was stolen from her.
As Victor prepares to drink the cup of poison to kill himself, Emily stops him and reunites him with Victoria. Barkis interrupts them, and Emily recognizes him as her former fiance - who is revealed to be the one who murdered her for her dowry. Barkis tries to kidnap Victoria at sword point, but Victor stops him and the two men duel. Emily intercedes to save Victor and Barkis mockingly proposes a toast to Emily, claiming she was "always the bridesmaid, never the bride."
He unknowingly drinks the cup of poison. The dead, now able to intercede, drag the "new arrival" back to the Land of the Dead for retribution for his crimes. Victoria, now a widow, is once again able to marry Victor.
Emily sets Victor free of his vow to marry her, giving the wedding ring back to Victor and her wedding bouquet to Victoria before exiting the church. As she steps into the moonlight, she transforms into hundreds of butterflies, presumably finding peace, as Victor and Victoria look on wrapped in each other's embrace.