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.

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.

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.

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.

Eiji Aonuma started developing Majora's Mask because he had no interest in remaking new dungeons for Ocarina of Time's Master Quest mode.

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.

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 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.

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

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

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.

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."

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.

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."

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 early versions of Majora's Mask, the moon had no face. This could be why some promotional art shows the moon with no face.

The five main areas mirror the five stages of grief.

Clock Town is denial; its residents continue their daily lives refusing to believe the moon will fall.

Woodfall is anger; the Deku king is trying to kill a young monkey who allegedly kidnapped his daughter.

Snowhead is bargaining; Darmani begs Link to bring him back to life.

Great Bay is depression; Mikau dies trying to save the eggs of his love interest Lulu, leaving her alone.

Ikana Valley is acceptance; the only thing Link has left to conquer is himself, facing his own grief at the loss of his friend. The friend who began the journey, Navi.

After receiving the Romani's Mask, if you protect Romani's Ranch from the invaders on the First Day, and help Cremia deliver the milk to Clock Town, you'll receive 1 of 3 rewards. Link can get either a Huge Rupee (worth 200 Rupees), some Chateau Romani, or a hug.

If Link receives the hug, Cremia will hold Link up close to herself and a message will appear saying "You did it! You helped Cremia!" "You feel all warm and fuzzy! inside! Sigh... You could get used to this!" The extra exclamation point after fuzzy was removed in later versions of the game.

After slashing a sign with your sword in Ocarina of Time, playing Zelda's Lullaby while near the sign will repair it. Once the song is finished, the solving a puzzle jingle plays and the sign magically repairs itself.

This same thing happens in Majora's Mask with playing the Song of Healing.

After slashing a sign with your sword, playing the Song of Healing while near the sign will repair it. Once the song is finished, the solving a puzzle jingle plays and the sign magically repairs itself.

This same thing happens in Ocarina of Time with playing Zelda's Lullaby.