According to Aonuma, Majora's Mask 3D began development immediately after The Legend of Zelda: Ocarina of Time 3D was released in 2011.

Nintendo of Europe made a commercial using Tomodachi Life's Concert Hall feature to celebrate the announcement of The Legend of Zelda: Majora's Mask 3D in 2014.

In the bomb shop in West Clock Town, a large apparatus resembling the front of a Nintendo Gamecube can be seen, complete with controller, memory card ports, and a Game Boy Player attachment. To the right of it, the player can find an Ultra Hand, a toy released by Nintendo in the 1960's.

A robotic Operating Buddy (R.O.B for short) can be found in the backroom of the Curiosity Shop. This can be seen when the player uses the spyhole.

Inside the bedroom in Mama's House at Romani Ranch, a toy version of Ganondorf's horse from The Legend of Zelda: Ocarina of Time can be found discarded in the corner near a cupboard.

In the Goron Shrine, a Wii remote can be found among the toys that belong to the crying Goron baby.

The Ten Billion Barrel, a 1980's puzzle toy marketed by Nintendo, can be found in the Clock Town Shooting Gallery.

In the original game, the Song of Double Time could be used to automatically jump to dusk on the current day or the dawn of the next day (depending on when it was used). Its functionality was changed in the 3DS version to a choice of any hour within the current day or to the dawn of the following day.

A number of changes to the save system were introduced in Majora's Mask 3D:
• Owl statues now save permanently and no longer end the game when used.
• Playing the Song of Time no longer saves the game.
• Like the original Japanese version, the game now has three save slots (up from the two in the US version - a result of adding owl saving which wasn't present in the Japanese release).
• Additional non-owl save statues were added to the game. These statues can be used to save but not for fast travel.

Hidden between the beakers in the Marine Research Lab in the Great Bay is a Love Tester, a product made by Nintendo in the 1960's.

Collecting the Hot Spring Water from Darmani's Grave during the final countdown on the last day can lead to some interesting glitches, including being able to transform into Feirce Diety Link early and being able to stop time itself.

It is possible to catch a fish named "Lord Chapu-Chapu" in one of the new fishing ponds, which resembles Lord Jabu Jabu from The Legend of Zelda: Ocarina of Time.

Inside the bedroom in Mama's House at Romani Ranch, a toy version of Link's horse, Epona, can be found on a shelf.

It's possible to catch a Great Fairy Fish in the Ocean Fishing hole. The player has to be wearing the Great Fairy Mask and needs to lure it out by catching a regular Fairy Fish first.

A pair of Zora flippers can be found in the Trading Post located in West Clock Town. This is a reference to the Zora flippers that have been used in other Zelda titles.

In the Nintendo 64 and 3DS versions of Majora's Mask, several real-life constellations can be seen in the sky as well as the rock formations on the Termina Field wall.

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.