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.

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.

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.

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.

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..."

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 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 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.

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.

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.

If the player talks to Keaton while wearing the Keaton Mask, he'll ask a series of questions. A sound is made signaling whether the answer selected is correct or incorrect. Picking the correct answer will trigger the "pause" sound from the game Excitebike on the NES.

During the final boss, there are flower symbols on the floor. The player can actually use these as Deku launch pads if they equip the Deku Mask.

On the morning of the 1st day, when the player finds Kafei going to the post box, using a bomb or the Blast Mask next to him will cause him to flash red as if taking damage.

On the back of Anju's grandmother's wheelchair, there's a picture of a tiger. This is a possible reference to the pet tiger owned by Granny in The Legend of Zelda: Ocarina of Time in Kakariko village, who is also Anju's grandmother's Hyrule counterpart.

There are 3 unused masks that can be found within the game's data that were likely supposed to have been worn by the Skull Kid. They're strange masks that look like Link, each rotated differently to be used in different scenarios.

If the player stands in the little garden outside of the Astral Observatory in Termina Field when the Clock Tower opens on the third day, a different cutscene will play that shows the tower opening as if looking towards Clock Town from the Observatory.

Through use of Gameshark or Action Replay cheats, it is possible to get "Saria's Song", as well as the "Sun's Song" from Ocarina of Time. The "Sun's Song" has no difference from Ocarina of Time, and fast-forwards time to the next day. "Saria's Song", however, doesn't do anything.

Each piece of music in the Zora Hall is taken from a previous game in the series. This includes the main hall being the Zora's Domain's music from Ocarina of Time, Tijo playing part of the cave theme from A Link to the Past, Japas playing part of the dungeon theme from The Legend of Zelda, and Evan playing the Game Over song from the same game.

The postman in Majora's Mask, who wants to flee, but can't find time for it in his schedule, shows quite the similarity to some couriers from a short story written by Franz Kafka. They want to kill themselves, but refrain from doing so due to their "oath of service".