Later that year it was again reissued (without the Master Quest add-on) on The Legend of Zelda: Collector's Edition as part of a limited-time promotion. The bonus disc also included the Ocarina of Time Master Quest, a previously unreleased version of Ocarina of Time with redesigned dungeons and supposedly greater difficulty. In 2002, Ocarina of Time was re-released as a bonus disc on the Nintendo GameCube for those who pre-ordered The Legend of Zelda: The Wind Waker.

The GameCube version is similar to 1.2 but has some differences including button icons changed to their GameCube colors. Also for version 1.2, the original theme for the Fire Temple, similar to an Islamic prayer chant, was replaced in version 1.2 with a new theme. Ganon's blood at the end of the game appears red in versions 1.0 and 1.1, but was changed to green in version 1.2.

Version 1.1 is similar to version 1.0 except the above glitch was fixed (there is, however, a different known method that works on all versions, including GameCube ones). The most notable difference between version 1.0 and the following versions is that in version 1.0, if one were to save and reset the game during the final Ganon fight, they would be able to play the game without Link's sword, which in turn would allow them to use any item on Epona. Version 1.1 grey cartridges began to be released in early 1999, in which Nintendo fixed a number of bugs and glitches from the first version. All of the gold cartridge games that came out in November 1998 are version 1.0, and some grey cartridges released soon after are also version 1.0. The game was also released in different software versions. Additionally, the game's box was made of sturdy plastic instead of cardboard and exhibited the boxed phrase 'Collector's Edition.' Gold carts were the first American release of Ocarina and were only offered in a limited number, making them collector's items. In keeping with the established Zelda tradition, pre-ordered copies of Ocarina of Time on the Nintendo 64 featured 'gold' cartridges. It is important to be specific when referring to the different versions of Ocarina of Time.

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