Although developed internally by Nintendo, Super Mario Bros. Deluxe did not see a conventional release in Japan. Instead, it was released in Japan on March 1, 2000, nearly a year after its American and European releases, exclusively for the Nintendo Power service, which allowed people to download games from kiosks onto Game Boy Memory Cartridges for lower prices.

Whenever there are new photos to view in the Japanese version of the game, the photo album has a flashing icon saying NEW above it that isn't present in other versions.

When the game was released on the 3DS Virtual Console, all renders of Multiplayer mode became unplayable, due to the 3DS not supporting any link or infrared capabilities that the Game Boy Color had originally. Because of this, strings referencing multiplayer modes in the Fortune Teller were changed to duplicate other Text Strings:

• "Today is your day to win the race" was changed to "Fortune is hidden in bricks unbroken".
• "Victory is yours in the coming race" was changed to "Feelings shared will be understood".
• "Trade high scores to set new goals" was changed to "Fortune is hidden in bricks unbroken".
• "A VS Mode victory is not your fate" was changed to "Stomping on spikes leads to sore feet".
• "Victory in a race may wash pain away" was changed to "Change old habits Yield new success".