The Song of Healing has the same first six notes as Saria's song but played backwards with a different rhythm.

According to the gossip stone in Romani Ranch in the Cucco Shack, the All-Night Mask was used as a torture device.

"A torture device of insomnia called the All-Night Mask seems to be available at the Curiosity Shop..."

When the thief Sakon tries to steal the bomb bag from the Old Lady from the Bomb Shop, if Link hits the Bomb bag with an arrow, the hookshot, or another bomb, the bag will explode, killing Sakon.

At the end of the game, Skull Kid asks Link to be his friend and says, "You have the same smell as the fairy kid who taught me that song in the woods." This hints at the Skull Kid being the same one that Link sold the Skull mask to and taught Saria's song in Ocarina of Time.

The arch at the entrance to Romani Ranch is actually the same arch at the entrance to Kakariko Village from Ocarina of Time. Even the text on the sign is re-used, effectively saying "Welcome to Kakariko Village" in both games. This is more noticable in the Japanese version, which features the text in Japanese instead of the localized version's Hylian text. The Hylian text still translates to "Welcome to Kakariko Village", though.

If Link is wearing the Captain's Hat during the fight with Igos du Ikana, a cutscene will take place where he will mistake Link for Captain Keeta, a military general for the Ikana. He then realizes that Link is too tiny to be Keeta and then resumes attacking Link.

In both 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.