Miyamoto had originally planned for "A Link to the Past" to have a party system where you could switch between three characters and utilize their individual abilities. The characters would have been a mix between an elf and a fighter, a magic user, and a girl.

There is an unused item called "The Letter" that occupies the same inventory space as the Magic Mirror. It uses the same sprite as the map, similar to the letter item from the original Legend of Zelda.

There is a secret room, called the Chris Houlihan room, that is not accessible via normal means. It contains a telepathy tile and 225 Rupees and is used as an error handler if you fall into a hole but the game can't find a proper destination.

This room appeared as a result of Chris Houlihan winning a Nintendo Power contest and being promised an appearance in a Zelda game. Many of the glitches used to access the room were removed in the GBA port though, along with any mention of Chris.

There are several portraits of Mario hanging in houses of Kakiriko Village, pulling on the portraits causes Rupees to come out.

Concept Art for A Link to the Past shows Zelda in futuristic attire. The original Legend of Zelda was planned to be set in both the past and the future. This art could be an indication that Nintendo considered reusing the concept for A Link to the Past.

An unused enemy soldier with a cannon is fully programmed in the game, but never used. He includes full AI, graphics and animations.

The Master Sword was named after King Arthur's legendary sword "Excalibur" in the French version of The Legend of Zelda: A Link to the Past. The name Excalibur would also be used in the French versions of The Legend of Zelda: The Wind Waker and The Legend of Zelda: Twilight Princess.

In a 2020 interview about Luigi's Mansion 3, the game's lead producer Kensuke Tanabe (who was also the scenario writer for A Link to the Past) compared a shift during the game's development to an early idea that was scrapped during A Link to the Past's development, revealing that the game originally had multiple parallel worlds but it had to be cut down to just two—those being the worlds of Light and Dark.

"When that happens, I try not to cling to that initial idea too much. For example, this is when I was working on The Legend of Zelda: A Link to the Past. At first, we were thinking about structuring the game with numerous parallel worlds. However, in order to establish the gameplay in the end, we decided that it would be better to narrow it down to two worlds: Light and Dark. I think game development involves much work where you never know unless you actually test it out."