There are 5 stary faily fountains in Majora's Mask, in Clock Town, Woodfall, Showhead, Great Bay, and Ikana Canyon. They all start off with 10 stray fairies except for the one in North Clock Town which starts off with 24. For each fairy fountain, after you bring all stray fairies from its corresponding area, a great fairy will appear give you a prize. The one in Clock Town gives you a half size magic meter if you don't already have magic and if you return the Clock Town stray fairy to her again with the Deku Mask, she will give you the Great Fairy Mask. The one in Woodfall gives you the Great Spin. The one in Snowhead gives you a full sized magic meter. The one in Great Bay gives you double defense, which does nothing other than change the amount of damage to Link damage sources do to exactly half what they would to without it. Link's health comes in eighths of a heart after the double defense upgrade. The one in Ikana Canyon gives you the Great Fairy Sword.

Each time you collect a stray fairy, it restores 3 hearts in the English version and 1 heart in the Japanese version. Stary fairies will come towards you when you're wearing the Great Fairy Mask. Collected stray fairies are lost and any already activated great fairies disappear when you play the song of time. Every time you go far enough into a fairy fountain, you bring all the fairy that you got that belong there that aren't already there there and if the number of them you got that aren't already there that belong there isn't 0, there will be a cutscene of you bringing them there. Every time you bring all the stray fairies that belong in a certain fairy fountain to that fairy fountain the first time in a cycle, a great fairy will appear there and also give you the prize she normally gives if you don't have it. The Great Fairy in North Clock Town will also give you the Great Fairy Mask if you go in there after having returned the stray fairy and then duped over the Great Fairy Mask in the same cycle but the one in Ikana Canyon will only give you the Great Fairy Sword the one time in the cycle when you return all its stray fairies to that fairy fountain and not when you go there having having returned them all then duped over the Great Fairy Sword in the same cycle. All stray fairy fountains will ease your weariness any time you go far enough in for the first time since entering except for times you get the Great Fairy Sword.