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Anime and Manga
- A Little Snow Fairy Sugar: The title character, using her flute to create snow.
- Fushigi Yuugi: Amiboshi
- Naruto: Tayuya is this and Musical Assassin. She can manipulate demonic dolls using it, as well as casting illusions.
- From Magi – Labyrinth of Magic, this is how Aladdin summons Uugo, and how Pisti can befriend animals.
- Mai-HiME: The mysterious white-cloaked HiME who uses a flute to control Yatagarasu. Better known as the Face–Heel Turn-ed Shiho.
- Lena of Shamanic Princess uses a flute to summon and manipulate a vine-like substance.
- In the Makaiju arc of The '90s Sailor Moon, Ail uses his flute and his Magic Music to summon and control the monsters of the week.
- In one of the Dragon Ball Z non serial movies, Future Trunks befriends one of these. His name is Tapion, he plays a magical ocarina and has one half of a God of Evil sealed in his body.
- The Smurfs and the Magic Flute and its 2008 prequel The Flute Smurfers. See also Western Animation.
- In The Courageous Princess, Irgerat usurped his brother's throne via a magic flute, that turns out to be able to summon literally any magic effect the player wants. The protagonist, after using it to defeat him and the dragon pursuing her, ends up breaking it in half since it's too powerful an Infinity +1 Sword for anyone to possess.
- The Pied Piper of Hamelin: The titular character is this.
Films — Animated
- Shrek Forever After: The Pied Piper is a bounty hunter, his flute adjustable to whatever creature he wanted to hypnotize (in this case, ogres).
Films — Live-Action
- The Dark Crystal - Jen's split flute comes in handy for identifying the true shard and in a bonding scene with fellow Gelfling Kira.
- Escape to Witch Mountain (1975): Tony plays a harmonica to increase his telekinetic powers.
- Kill Bill - Bill plays a wooden flute which lends to his mysteriousness.
- Live and Let Die: One of James Bond's opponents is a man who plays the role of the voodoo loa Baron Samedi. Bond once encounters him while he's playing a flute. After apparently being killed by venomous snakes, at the end he appears riding the front of a train, indicating that he may be the real Baron Samedi.
- Willy Wonka & the Chocolate Factory: Mr. Wonka uses a flute key to summon the Oompa-Loompas when he needs to issue a command to them.
- 7 Faces of Dr. Lao: Pan uses his pipes on Angela as the audible equivalent of a Love Potion (though he ultimately points her towards her local would-be suitor rather than himself.)
- Edgar Pangborn: His short story "Tiger Boy" might count. The eponymous youth plays a set of pan pipes, runs wild and naked, and has a fully-grown tiger as a companion. The pipes attract a mute teenage village boy to Tiger Boy's side (possible echoes of the Pied Piper). However, he's not actually magical - it's a feudal, post-holocaust world. (He's certainly not immortal either.)
- The Elenium: A young girl ,the Goddess Aphrael, who seemingly doesn't talk but does play the flute is named Flute by our heroes.
- The Lion, the Witch, and the Wardrobe: The faun Mr. Tumnus (the first Narnian we meet) played a flute lullaby to Lucy on her first trip to Narnia.
- Percy Jackson and the Olympians: Grover the Satyr often uses flutes (all versions of them, in fact) to cast nature-based spells. Among them include one that causes a Titan to assimilate into an enormous oak tree during the final battle with Kronos. That's what I'd call a Fate Worse Than Death.
- Xanth: Chester Centaur's magical talent is to manifest and play a magical flute.
- The Rat Piper in The Amazing Maurice and His Educated Rodents (the real one, not the stupid-looking kid) works very hard at maintaining this image. Maurice and Keith trade on his reputation.
- The Blind Idiot God Azathoth in the Cthulhu Mythos enjoys himself some flute music, which undoubtley be at least extremely unpleasant to human listeners.
- The Piper of Keys to the Kingdom, who is based on The Pied Piper of Hamelin, uses his pipes to control children and rats.
- In Ruth Frances Long's The Treachery of Beautiful Things, playing the flute in the woods is what led to Tom's capture by The Fair Folk.
- In Rachel Griffin, Rachel initially uses a flute to cast spells, as per the trope. However, it turns out that just whistling can do as well.
- Pact has Johannes Lillegard, a sorcerer who wields a set of pipes which are said to have originated with the original Pied Piper. He uses them to control rats, dogs, and the copies of children whose suffering he sells to supernatural creatures for power.
- Virginia Dare in The Secrets of the Immortal Nicholas Flamel apparently plays her flute for a living. She also uses it to cast spells.
- At one point in the story of This Immortal, the group of protagonists encounters some satyrs in the forest, prompting Conrad to produce shepherd's pipes out of nowhere and causing a dancing frenzy among the satyrs with his music. At the end of the book, Myshtigo theorises that Conrad may be the god Pan in disguise when recalling that incident.
- In the Felix Castor series of novels, the titular character favored medium of channeling his ability to bind ghosts is by playing tunes on a tin whistle that reflects the ghost's nature.
- In the Bedlam's Bard series by Mercedes Lackey, the main character Eric Banyon is a Bard whose primary instrument is the flute.
- In the Elemental Masters series, Air Master Nigel Barrett uses a flute for such spells as summoning the sylphs. He started out with a metal one, but when it didn't feel quite right, he had a glassblower make him a glass one instead.
- Fraggle Rock: Cantus played a magical forked pipe.
- The Magic Flute: Naturally, and there are also magic bells involved.
- The Magnus Archives:
- The war poet Wifred Owen has an encounter on the battlefield with a strange being he calls the Piper.
- The title of the episode "Boatswain's Call" refers to the old-fashioned whistle the mate carries. The narrator soon learns that it's no ordinary call.
- Fire Emblem Elibe: The Wandering Minstrel Nils plays the flute, allowing one character to make an extra move, and later in the game, providing status buffs. By contrast, his older sister Ninian does the same with a Magic Dance.
- The Legend of Zelda series: Link, although he himself is not very mysterious since he is the player-character. His instrument also varies from game to game: recorders, ocarinas, pan pipes, etc. Sometimes, though, such as in The Legend of Zelda: A Link to the Past, Link gets his flute from a character who plays this trope straight.
- Mushihime Sama BUG PANIC!: A mysterious girl who appears in the cutscenes named Sora
- NiGHTS: The eponymous character himself/herself plays the invisible flute.
- Ōkami: Waka, who provides the page image, is named after a form of Japanese poetry. His appearance is always announced by the sound of a flute, and he tells cryptic, yet accurate prophecies.
- Onmyōji: Ōtengu uses his flute to cast a hypnotic spell over unsuspecting yōkai.
- Mannen-dake is the only flutist in the game who actually uses the instrument as a weapon.
- Seiken Densetsu 3: A magic flute summons a big goggles-wearing turtle at beaches.
- Super Mario Bros. 3: A magic whistle can be used to skip whole worlds.
- Dynasty Warriors: Zhen Ji's primary weapon is a magic flute that she also uses to hit people over the head.
- Final Fantasy IX: Eiko, a white mage and summoner, can use flutes as weapons.
- Wario Land 3: At one point, Wario must play on a flute to summon the Fire Snakes from their pots so they can be used as platforms.
- Illusion of Gaia: Will uses a flute both to play magical songs and as a blugeoning device.
- Looney Tunes: A few shorts have parodied The Pied Piper:
- Porky Pig played the Piper in a couple of cartoons. In one he has to contend with a cat angry with him for ridding Hamelin of rats.
- Sylvester tried to make a flute to capture Speedy Gonzalez and friends. Also, Sylvester Jr. found that he could attract different animals by adding holes to the flute.
- The Smurfs and the Magic Flute: Peewit stumbles upon the magic flute of the Smurfs that makes whoever listens to it dance to its tune. It ends up in the possession of a thief named Matthew McCreep, who uses it to make people pass out from the dancing so he can rob them.
- In ThunderCats (2011), Wileykit can send people into a trance by playing a sort of ring-shaped ocarina.
- The Pixie & Dixie short "Pied Piper Pipe" has Mr. Jinks, inspired by the Pied Piper story, create a flute to torture the meeces with. They get back at him by placing a dog whistle in the flute so Jinks can get beaten up a nearby bulldog.
- The 1930 Screen Songs short "In the Good Old Summer Time" has a gag where a hippo's flue brings inanimate objects to life and follow him. Even a stereotypical Jewish pig's clothes fly off of him to follow the sound.
- The Adventures of Puss in Boots has the Piper Maliflua, who can control animals with her flute like the Pied Piper, but only one kind of animal at a time; she uses a different flute for each animal.
- Kaeloo: In Episode 132, Mr. Cat somehow gets hold of a magic flute and tries to use it to lead a bunch of sheep into a trap.
- The Japanese shakuhachi is strongly associated with the Fuke sect of Zen Buddhism, who used the instrument as part of their meditative process. When the Meiji government cracked down on the previous bakufu and all associated religions, they specifically attacked the practice of playing the shakuhachi.