If the Song of Healing 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 with Left, Right and Down.

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 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.

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..."

There's unused text regarding getting a seahorse in a bottle. In the final game, the player must have an empty bottle to get a seahorse.

"You traded for the Seahorse.
And it came in a bottle!
You should hurry and return it
to its home at Pinnacle Rock."

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, Spoiler:Link must help Kafei retrieve a wedding mask so that he can marry Anju mere minutes before the moon is set to annihilate Clock Town.

In the North American commercial, a woman can be heard saying "Though I walk through the valley of death, I shall fear no evil."

This is a paraphrasing of the first half of the Bible verse Psalms 23:4, "Yes, though I walk through the valley of the shadow of death, I will fear no evil: for you are with me; your rod and your staff they comfort me."

An unused fishing mini game can be found in the game's data. It would have been similar to that of the fishing in Ocarina of Time. Fish and the owner of the fishing mini game can be spawned into the game by modifying the data, but using the fishing rod will frequently cause the game to crash.

Zelda was originally going to use a flute to teach Link the song of time, but the instrument was swapped for an ocarina.

One possible reference in the game occurs during the final boss fight against Majora's Incarnation; he sometimes hums what sounds like the melody to the Death Mountain Dungeon from the very first Legend of Zelda

After Kafei gives Link the Pendant of Memories, he asks Link to keep it "a secret to everybody", a reference to the popular quote from The Legend of Zelda.

During early trailers of the game Zora link, Deku Link and Goron Link had their instrument icons instead of the ocarina. It's unknown why this feature went unused in the original game but it was later reused in the 3DS remake.

After playing the Song of Soaring, the map that displays locations Link can travel to comes up. The locations of the Southern Swamp and Windfall are displayed incorrectly. The Southern Swamp is shown to be east of Woodfall, but the player must travel east from the Southern Swamp in order to go to the Old Hags Potion Shop, Deku Palace and Woodfall.
This was corrected in the 3DS remake.

Two screenshots found on the game's Japanese website show Link confronting Skull Kid on top of the Clock Tower during the day. This is impossible in the final game without the use of a glitch or cheat device.

Originally, the in-game three-day system was going to be a week, but Eiji Aonuma, the game's director, thought that player's would be annoyed having to go through an entire week again and it would be hard to remember what happens each day.

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.