In both Pokémon Red and Pokémon FireRed, the Poké Flute is rewarded to the player after rescuing Mr. Fuji from Team Rocket in the Pokémon Tower. To be awarded the Poké Flute, obtain the Silph Scope, journey to the Pokémon Tower, battle Marowak with the Silph Scope and defeat all of the remaining members of Team Rocket. Talk with Mr. Fuji until he gives you the Poké Flute.Continue Reading
After defeating the Team Rocket head Giovanni, acquire the Silph Scope from the Rocket Hideout.
The Pokémon Tower is the tall tower in Lavender Town, in the region of Kanto. Go to the top floor of the tower. At the exit to that floor, meet the ghost.
Use Silph Scope against the ghost until it presents itself as Marowak. Defeat the Marowak in battle to unlock the exit to the next area. Note that Pokéballs are wasted on this Marowak, so do battle with them.
A few Team Rocket members are spread around the next area. Defeat them all.
Once the area is cleared of Team Rocket, find Mr. Fuji. After talking with him the first time, he takes you to his house. When you talk to him again, he awards you the Poké Flute.