In The Legend of Zelda: Ocarina of Time, Link received the Fairy Ocarina fairly early on in the game when Saria handed it over to him prior to venturing out into Hyrule Field. When Princess Zelda and Impa escape Hyrule Castle, the princess tosses the Ocarina of Time into the moat surrounding the castle. Once Link acquires the Ocarina of Time, he will no longer use the Fairy Ocarina.
In Picross NP Vol. 5, a video game released on the Super Famicom's Nintendo Power, the Fairy Ocarina is the second of the twelve "Character Mode" puzzles, despite not actually being a character. It, the Keaton Mask, and the Fairy Slingshot are all puzzles that are actually items rather than characters in the game.