A Spanish localization for The Legend of Zelda: Ocarina of Time was planned by Nintendo of Europe's Madrid branch, only to be scrapped partway through due to production difficulties faced by the main development team in Japan. Consequently, the Spanish release of the game used the English-language ROM, bundling the cartridge with a 150-page booklet containing all of the game's text in both English and Spanish. The cumbersome nature of the guide and the potential risk of encountering spoilers while flipping through it was considered enough of an issue that Spanish advertisements for The Legend of Zelda: Majora's Mask heavily emphasized the inclusion of a proper localization. Despite this, the guide's Spanish-language text was not added back in for the Virtual Console re-releases of Ocarina of Time.

The Goron Tunic, meant to protect Link from heat and reduce damage taken from lava, also affords the same protection against acid and spikes due to both being coded to use the same hit detection as lava.

While Link being able to manually jump either on his own like in Zelda II: The Adventure of Link or through the use of an item like the Roc's Feather from The Legend of Zelda: Link's Awakening is a recurring ability in the series, several 3D installments forgo this in favor of having Link jump automatically at the edge of a platform. There are conflicting claims by series producer Eiji Aounuma and series co-creator Shigeru Miyamoto as to who thought of the automatic jump during the development of The Legend of Zelda: Ocarina of Time and why. Aonuma claimed the autojump was directly inspired by the Roc's Feather and he had it implemented due to his own poor ability at playing platform games, wishing that the game could do the jumping for him. Miyamoto on the other hand claimed that he had thought of the autojump one morning and sprung it on the development team, who were planning to add a manual jump and were previously used to making Mario games, as an intentional limitation to see if they could "do all kinds of things." Manual jumping would be incorporated into a 3D Zelda game for the first time with The Legend of Zelda: Breath of the Wild.

If the Song of Healing in The Legend of Zelda: Majora's Mask is reversed, it sounds similar to Saria's Song from The Legend of Zelda: Ocarina of Time. While this may seem unintentional, the inputs to perform each song are also reversed from each other, with Saria's Song being played by pressing Down, Right and Left, while the Song of Healing is played by pressing Left, Right and Down.

If the game detects that its cartridge is a pirated copy, Zelda's hair will turn into a giant pentagon in cutscenes, fishing will always result in a hooked fish escaping after 51 frames of animation, and Spoiler:the exit to Ganon's Castle during the escape sequence will be blocked off to Link, as Zelda will run right through the bars, leaving Link behind and making the game impossible to finish.

In a 1999 interview published in a Japanese strategy guide for Ocarina of Time, series creator Shigeru Miyamoto revealed that Chain Chomps from the Super Mario Bros. series were planned to appear as enemies in Gerudo's Fortress. According to Miyamoto, the Chain Chomps would be able to capture Link and wrap him up in chains, requiring him to use the Megaton Hammer to break them and free himself. Chain Chomps were present up until the final revisions of the game; Miyamoto did not explain why they were removed.

Much like how Bowser's laugh in Super Mario 64 is sped up for use as the Boo's laugh, Ganondorf's laughter is sped up to create the laughter of the Poe Sisters in the Forest Temple.

The knight Link is fighting in the early Zelda 64 trailer uses the same texture as Metal Mario from Super Mario 64.

Taking out a Deku Stick near a group of butterflies and leading one away from the group will result in the butterfly turning into a Fairy.

The bassline for the The Song of Storms sounds very similar to the bassline for the Castle Theme from Super Mario World 2: Yoshi's Island.

Link was able to ride Epona into Hyrule Castle Town during later beta-builds of the game. This can be seen in various pre-release trailers. Why it was removed is unknown.

The owl that follows Link throughout his quest Spoiler:is actually the light sage Rauru.

Eiji Aonuma started developing Majora's Mask because he had no interest in remaking new dungeons for Ocarina of Time's Master Quest mode.

In early versions of the game Sheik's eyes were blue, but were changed to the red in the final version.

In early trailers of the game Link's bombs were slightly different. They were more round and a much darker blue.

According to an interview with Shigeru Miyamoto conducted while the game was still in development, Navi was originally intended to have romantic feelings for Link and was even jealous of Princess Zelda. Though it seems that these details were left out in the final game.

Dark Link mimics all of the player's moves and actions (save for a few.) The amount of health he has also corresponds to the amount of Heart Containers the player has by the time they fight him, potentially making him very durable or quite weak.

In early footage's of the game the spirit temple's boss door was a regular door instead of the huge designed door with a lock on it found in the final release.

In early versions of the game the shooting gallery mini game had more things Link can shoot instead of just rupees. Footage shows Link shooting bombs and other targets which are not in the final version of the game.

Epona, Link's horse, actually began as an idea discussed during development of Super Mario 64 to include a ridable horse in the game. While never included in Mario 64, the developers knew they would eventually include a horse in Ocarina of Time and planned for it from the very beginning.