In the game, there are unused cutscenes that show the Great Fairy training Link for his new abilities instead of just magically giving them to him.

The development for Majora's Mask started out of a lack of enthusiasm to work on the unreleased expansion for Ocarina of Time for the Nintendo 64 Disc Drive, dubbed "Ura Zelda". Eiji Aonuma protested the expansion, so Shigeru Miyamoto challenged him to make a sequel for the game within 1 year, in exchange, they would no longer have to make Ura Zelda.

In the Astral Observatory, there is a picture of a dolphin hidden under a small pot. It's thought to be a reference to Dolphin, the Gamecube's code name at the time.

If Link is wearing the Garo's Mask, the Gibdo Mask, or the Captain's Hat in the presence of Redeads, they will start dancing.

During development, Majora's Mask went by the name Zelda Gaiden. It was being developed for the failed Nintendo 64 Disk Drive add-on, and was to take full advantage of the hardware. The player originally had seven days to complete the game rather than three and it used the Disk Drive's internal clock to play out in real time.

All 4 main dungeon items pertain to the Bow. Woodfall Temple features the bow itself, while the Snowhead Temple has Fire Arrows, the Great Bay Temple has Ice Arrows, and the Stone Tower Temple has Light Arrows.

Aside from owl saves, the American release of Majora's Mask had a number of other changes made to it, both aesthetically and to its game-play, such as making dungeons easier, or simply moving objects around.

The impermanent flow of time in the first three-day cycle as Deku Link is 1.66 times faster than normal, meaning it takes only 27 seconds for each game hour to pass rather than the standard 45 seconds for every three-day cycle after it. It is in this stage of the game where NPCs and most enemies are not rendered outside of Clock Town's boundaries.

The Song of Healing has the same first six notes as Saria's song but played backwards with a different rhythm.

According to the gossip stone in Romani Ranch in the Cucco Shack, the All-Night Mask was used as a torture device.

"A torture device of insomnia called the All-Night Mask seems to be available at the Curiosity Shop..."

When the thief Sakon tries to steal the bomb bag from the Old Lady from the Bomb Shop, if Link hits the Bomb bag with an arrow, the hookshot, or another bomb, the bag will explode, killing Sakon.

At the end of the game, Skull Kid asks Link to be his friend and says, "You have the same smell as the fairy kid who taught me that song in the woods." This hints at the Skull Kid being the same one that Link sold the Skull mask to and taught Saria's song in Ocarina of Time.

The arch at the entrance to Romani Ranch is actually the same arch at the entrance to Kakariko Village from Ocarina of Time. Even the text on the sign is re-used, effectively saying "Welcome to Kakariko Village" in both games. This is more noticable in the Japanese version, which features the text in Japanese instead of the localized version's Hylian text. The Hylian text still translates to "Welcome to Kakariko Village", though.

If Link is wearing the Captain's Hat during the fight with Igos du Ikana, a cutscene will take place where he will mistake Link for Captain Keeta, a military general for the Ikana. He then realizes that Link is too tiny to be Keeta and then resumes attacking Link.

If the player equips the Bremen Mask and plays the marching melody during the Ikana Warriors mini boss battle, they will march with Link. It's quite handy to leave them open for an attack. However, it won't work with the following mini boss, Igos du Ikana, as he'll just attack Link regularly.

In a prerelease trailer for Majora's Mask, there seems to be an unused mask that looks like Adult Link for Ocarina of Time. This mask was rumored to be a transforming mask which would turn Link into Adult Link, allowing him to use certain items. The mask was removed before the final version and young Link is capable of using all of the items directly.

In the Japanese version, the cry that Skull Kid makes when attempting to crash the moon into Termina is coded as a sound effect associated with his actor. Consequently, the noise becomes significantly quieter when the camera cuts to a close-up of the moon's face. In the international release, this is adjusted so that Skull Kid's cry is instead coded as a global sound effect, ensuring that its volume remains consistent throughout the cutscene.

Depending on what you name your save file, the name inputted will act as a seed that determines the position of the twinkling white stars in the night sky, while the blue stars and larger red planet remain in the same position. Since there is a character limit of 8 characters for a name, the number of possible variations is estimated to be somewhere under 5.3 billion, the key word being "under" as this cosmetic feature does not utilize all 127 characters available, so the actual number is bound to be lower. This feature was explained to the Japanese audience at launch, but this was not known in the West until 2021.

Although Majora's Mask is a direct sequel to Ocarina of Time, there was an officially licensed novel released set shortly after the events of Ocarina of Time. "Link and the Portal of Doom" was written by Tracey West and published by Scholastic in 2006 as part of the Nintendo Heroes series. In the book, a mysterious portal suddenly appears in Hyrule which absorbs all things around it and threatens to destroy the land. Link and Navi have to travel across Hyrule to learn five parts of a song which will destroy the portal. Although officially licensed by Nintendo, it's considered to be non-canon.

In an article for the September 2000 issue of Nintendo Power, Jason Leung, the writer for the game's English-language script, claimed that the South Clock Town Business Scrub's allusion to his work keeping him away from his wife is a nod to the tribulations that the developers at Nintendo of Japan were going through while working on the game.