In the Nintendo 64 game, Adult Link's earrings are blue; Adult Link's earrings are silver in the 3DS version.

The 3DS version is used for the Epona trophy in Super Smash Bros. for Nintendo 3DS and Wii U, with Link wearing silver earrings.

As Adult Link, stepping on the ice where Lord Jabu Jabu was during Young Link's trip to Zora's Domain in a certain way will trigger a glitch and transport Adult Link to the "Inside Jabu-Jabu's Belly" dungeon. The dungeon remains fully explorable, but no new chests appear, nor does the boss and miniboss.

Almost none of the Nintendo 64 version's bugs were fixed. Nintendo did this to give players the same experience as in the Nintendo 64 version of the game, going as far to say they were fun.

The Happy Mask Salesman's Shop was updated in this version of the game to include all the masks that he carried on his backpack in Majora's Mask, lined up on each side of his shop. The backpack itself is lying on the ground behind him, and can be easily seen while speaking to him.

In the Hyrule Castle courtyard, in one of the windows you can see a Mario level background with warp pipes and blocks. This background replaced pictures of Mario, Luigi, Yoshi, Peach and Bowser from the original Ocarina of Time.

In the 3D version of Ocarina of Time, there are three hidden images in the game showing concept art of Link from Skyward Sword. These were likely included due to both games being developed around the same time.