In Pokémon X and Y, the player has to deliver the Poké Flute from the Parfum Palace to its owner, a Black Belt, who uses it to wake up a Snorlax that is blocking Route 7. The player does not get to keep the Poké Flute after they deliver it.
If the player uses the Poké Flute outside of battle, it will play a "catchy tune", but does not wake up any of the player's Pokémon.
A Poké Flute is a reusable item that cures all Pokémon in the battle of sleep, including the opponent's Pokémon. If no Pokémon are asleep, it will have no effect on the battle, but still counts as the player's turn.
Playing the Poké Flute will wake up sleeping Pokémon and may make them dance or pose for the player. There are three songs which the Poké Flute can play in this game, and Pokémon respond differently to each.
A Poké Flute belonging to a hippie appeared in Wake Up Snorlax!. He uses it to perform musical numbers in exchange for food. He also used it to wake up a Snorlax that turned out to be his Pokémon and was believed to be blocking a river.
Another Poké Flute appeared in Awakening the Sleeping Giant!, under the ownership of Lord Shabboneau. It is used in an annual festival involving a Snorlax living in the area near Camphrier Town, but, unfortunately, it had been taken away by the egocentric Princess Allie from the Parfum Palace. After a series of many-sided events, Ash and his friends managed to get the Flute back and return it to Lord Shabboneau so he could start the festival. Team Rocket, believing the Flute could actually control Snorlax, tried to steal it in order to gather themselves an army of Sleeping Pokémon, but the Flute was soon recovered, allowing the festival to be successfully completed.
The Poké Flute is used to wake sleeping Pokémon. Snorlax will only awaken to this flute.
This concludes the entries from the original series.
In Pokémon Origins
The Poké Flute in Pokémon Origins
The Poké Flute was seen two times, although briefly, in Pokémon Origins. It first appeared close to the end of File 2: Cubone, where Mr. Fuji gave it to Red as a thanks for saving him and the Pokémon Tower from Team Rocket. Red later used the Flute in File 3: Giovanni to wake up a Snorlax, which he then presumably caught.