The gameplay for the remaster is very similar to the original version, but it made some modifications to the game. One new feature is the use of the touchscreen to manage inventory items. Also, the touchscreen is used at times to play the Ocarina songs.[6] The game uses the system's gyroscopic technology to look around and aim the player's bow, boomerang, hookshot, longshot, and slingshot in first-person mode, unless the player chooses to use the classic analog stick control to aim.[7][8]
The 3DS version has the modified Master Quest dungeons and mirrored overworld in addition to the original game, and a new "Boss Challenge" mode that allows the player to fight all of the bosses one at a time, or in sequential order, while the Master Quest has its own version of the "Boss Challenge" mode, where the boss arenas are mirrored and enemies will do twice the usual amount of damage.