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- The episode Lupin III: The Woman Called Fujiko Mine "Vissi d'arte, Vissi d'amore" is a reference to the book. The phantom turns out to be the boyfriend of the opera singer Aiyan, who is living underground with him since people wouldn't approve their relationship.
- The Phantom is a minor character in The League of Extraordinary Gentlemen.
- During "The Witch and the Warrior" Wonder Woman's fight with a brainwashed Superman takes them past a billboard advertising the Broadway musical the Phantom of Gotham, complete with a white mask and red rose on a black background.
- Goosebumps: The book "Phantom of the Auditorium" centers around a ghost haunting Brooke and Zeke's middle school when their class decides to revive a cancelled play from 70 years ago.
- Phantom is based on the original novel with influences of the musical.
- The Phantom of Manhattan serves as a sequel to the musical.
- Maskerade is Terry Pratchett's Discworld parody of the novel.
- Doctor Who: A couple of times.
- The story "The Talons of Weng-Chiang" partially homages the novel with its plot element of a hideously-disfigured madman hanging around a nineteenth-century London music hall.
- In "The Caves of Androzani", horribly-scarred and masked Anti-Villain Sharez Jek has a Stalker with a Crush fixation on the Doctor's companion Peri which is obviously inspired by Erik and Christine.
- Iron Maiden includes a song called "Phantom Of The Opera".
- Roommates features characters from the novel as regulars.
- American Dad!: In "The Phantom of the Telethon", Roger dresses up as the Phantom to sabotage Stan's telethon as revenge for stealing his idea.
- Arthur: In "Love Notes for Muffy", Francine tells the Brain to let go of his grudge against Muffy before he "becomes some crazy guy living up in the school rafters dropping chandeliers on people."
- Count Duckula: has the Phantom and his manservant as guest villains in the episode 'A Fright at the Opera.' They reappear in the Villain Team-Up episode 'Venice a Duck Not a Duck'.
- The Real Ghostbusters: in episode, also called 'A Fright at the Opera' the ghostbusters have to deal witha bunch of ghostly Valkries. The Phantom appears at the end, leaving in a huff due to the noise.
- Family Guy: A Cutaway Gag from "Deep Throats" features Peter and Lois attending the Andrew Lloyd Webber's musical, and Peter demands that the Phantom reveal the ugly side of his face so he can leave. "That nose better be piggy!"
- In an episode of Milo Murphy's Law, Milo and Melissa go to see Llamalet, Shakespeare's Hamlet with an all-llama cast. On their way to the theatre, posters are seen for a number of similar shows, including Phantom of the Llama. Melissa notes that some of the titles were better than others.
- Oswald the Lucky Rabbit: The 1930 short Spooks is a parody of the 1925 film (which was being reissued with sound that same year).
- In the Musical Episode of Phineas and Ferb, Phineas' number includes a montage of the boys homaging various musicals, including himself as the Phantom and Ferb as Christine.
- The Powerpuff Girls (2016): In "Bubbles of the Opera", Bubbles wears a half-mask, hood and cape to hide her disfigured face.
- Scooby-Doo! Mystery Incorporated: The episode "In Fear of the Phantom" is about a phantom controlling a theatre, causing accidents and kidnapping a young female singer.
- The Simpsons:
- In "Flaming Moe's", Homer imitates the Phantom when he reveals the secret ingredient of the Flaming Moe to everyone.
- In "Lisa's Wedding", it is shown that Martin Price faked his death in the future and is now living below the school à la the Phantom. He ends up playing "A Fifth of Beethoven" on his pipe organ.
- In "The Italian Bob", Krusty lets the Simpsons appear in his Roman opera to protect them from Sideshow Bob, and Homer asks if he can play the Phantom.Lisa: Dad, the Phantom isn't in this.Homer: But I do a great impression of him. "A-a-a-a-h! I am the gayest supervillain ever!"
- In Guillermo del Toro's opening for "Treehouse of Horror XXIV", Mr. Largo is conducting four different Phantoms (three as played by Lon Chaney, Herbert Lom and Claude Rains, plus one based on the cover of the original novel).
- SpongeBob SquarePants: In "Something Smells", Patrick walks on SpongeBob, who believes he is ugly, hiding in his house playing a pipe organ while wearing Groucho glasses.
- Teenage Mutant Ninja Turtles: in the episode 'Phantom of the Sewers'. Shredder even posed at the Phantom in another episode.