The secret ending, "Another side, Another story," was not meant to be a real game. It was only there to show off ideas that Tetsuya Nomura had for the sequels. It was not until Kingdom Hearts 358/2 Days that the fight shown was playable.

Bahamut, a recurring summoned creature from the Final Fantasy series, was planned to be a summon for Sora. But it was removed from the final version. Searching through the game data, a Bahamut summon option can be chosen through the use of cheat codes. However, since there is nothing to execute when it is chosen, the game will crash.

According to some concept art released by Square Enix, Sora was originally not going to wield a Keyblade at all, but a chainsaw sword instead. He was also going to have a design with lions fur, claws, a tail and ears.

Sora was not originally the main protagonist of the series. In the beginning, Disney had desired Donald Duck to be the protagonist, while Squaresoft wanted Mickey Mouse. Series creator Tetsuya Nomura wanted neither and developed an original character based off of Disney's style. In the end, Sora was created. His yellow shoes, red shorts and white gloves are based on Mickey Mouse.

In the Secret Place, on Destiny Islands, the walls are covered in paintings which seem to foreshadow some of the earlier events in the game. For instance, there is a painting of Sora winning at the coliseum; the tree house from Deep Jungle; and Pluto waking Sora up in Traverse Town.

Before the game was released in the U.S., Square held a "Name-in-Game" contest. A person named Kurt Zisa won the contest, and his name was used for a hidden boss in the game.

According to series producer Tetsuya Nomura, one reason that Mickey Mouse's role was limited in the original Kingdom Hearts was because around the same time as its release, Capcom owned the license to use Mickey Mouse for the game Disney's Magical Mirror Starring Mickey Mouse. The developers persisted and were eventually given the go-ahead to add him into the game "as long as [they only had him in] one scene, from far away, as a silhouette, with him waving his hand or something". As such, Mickey only appears briefly and seen from behind near the end of the game, helping Sora and Riku seal Kingdom Hearts itself.

Mickey's perspective of this event also appears in Kingdom Hearts 0.2 Birth by Sleep: A fragmentary passage. The reason that Mickey loses his shirt is to partially keep the continuity of the original Kingdom Hearts that showed Mickey in his classic shirtless look.