In the game's files are unused graphics that say "Game Over" and "Continue Playing?" In the final game, losing all of the player's hearts will warp said player back to the beginning area, and Spoiler:letting the moon fall will result in a lengthy cut scene followed by the famous words, "You've met a terrible fate, haven't you?" accompanied by the Happy Mask Saleman's chuckle.

In the game's files is unused text regarding the player's stolen Hero Shield. It's suggested that the shield would've been stolen, resulting in the player going to the Curiosity Shop to get it back.

"You bought back the Hero's Shield
that was stolen from you.

In the future, watch out for
swooping birds on your travels."

In the game's files are two unused texts regarding the Hylian Loach. This may suggest that said fish would've been found in both a bottle and without one.

The first text states:
"It's a Hylian Loach in a bottle!
An illusory fish that
few have caught...

And it came in a bottle!
What a find!"

Another one states:

"You got the Hylian Loach!
An illusory fish that
few have caught..."

Inside the moon, there is a bird that flies around the tree on the plain. This bird was originally in the beta version of Ocarina of Time, but went unused and was repurposed for Majora's Mask.

Eiji Aonuma has stated that Anju and Kafei's characters were inspired by the 1998 North Korean Taepodong missile crisis. During the game, Link must help Kafei Spoiler:retrieve a wedding mask so that he can marry Anju mere minutes before the moon is set to annihilate Clock Town.

If the Song of Healing in The Legend of Zelda: Majora's Mask is reversed, it sounds similar to Saria's Song from The Legend of Zelda: Ocarina of Time. While this may seem unintentional, the inputs to perform each song are also reversed from each other, with Saria's Song being played by pressing Down, Right and Left, while the Song of Healing is played by pressing Left, Right and Down.

The aliens that attack Romani Ranch during the first night are based on the Flatwoods Monster, an alledged alien being that was reported to have been sighted in the town of Flatwoods, West Virginia, USA, on 1952.

A Spanish localization for The Legend of Zelda: Ocarina of Time was planned by Nintendo of Europe's Madrid branch, only to be scrapped partway through due to production difficulties faced by the main development team in Japan. Consequently, the Spanish release of the game used the English-language ROM, bundling the cartridge with a 150-page booklet containing all of the game's text in both English and Spanish. The cumbersome nature of the guide and the potential risk of encountering spoilers while flipping through it was considered enough of an issue that Spanish advertisements for The Legend of Zelda: Majora's Mask heavily emphasized the inclusion of a proper localization. Despite this, the guide's Spanish-language text was not added back in for the Virtual Console re-releases of Ocarina of Time.