Although the game was developed by Capcom, it was published by Nintendo as part of an exclusive deal they made with Disney in 1999 to publish Mickey Mouse titles for the Nintendo 64, Game Boy Color, and the still in-development Nintendo GameCube. As a result, Nintendo has a small section before Capcom in the game's end credits, featuring producer credits for Hiroshi Yamauchi, Shigeru Miyamoto, and Kenji Miki.

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.

In the game's files is an unused title graphic for when the game was initially called "Disney's Mickey for Nintendo GameCube."