The Western version of the music that plays in the cutscene after clearing all 96 exits has a portion that contains the level clear theme from the original Super Mario Bros..

In the SNES game, the Boos and Big Boo are light blue. In the Game Boy Advance game, the Boos and Big Boo are white.

Bowser and the Koopalings all have 3 fingers on their hands in the SNES game. In the Game Boy Advance game, Bowser and the Koopalings all have 4 fingers. His arms were also recolored.

In the SNES game, all of the Yoshi eggs have dull brown spots on them (besides Green Yoshis). In the Game Boy Advance game, the Yoshi eggs all match the color of the Yoshis inside them.

In the Game Boy Advance game, Princess Peach has blue earrings, lighter hair and a lighter pink dress. These changes more accurately represent Peach's current look. In the SNES game, Peach has pink earrings along with a darker pink dress and hair.

A power-up can be found lying on the ground in the last room of #3 Lemmy's Castle. In the SNES game, the power-up is super mushroom; in the Game Boy Advance game, the power-up is a feather.

In the SNES game, when fighting Bowser, only the box with the reserve item appears at the top of the screen. In the Game Boy Advance game, the full HUD is displayed.

In both versions of the game, the seventh room of Bowser's Castle contains statues that spit out flames. The first statue in that room, which appears in the SNES game, is missing in the Game Boy Advance version.

The player can re-play a castle by simultaneously pressing the L and R buttons in the SNES game. In the Game Boy Advance game, the player cannot re-play a castle until Bowser is defeated; after Bowser is defeated, the player can then re-play the castles by entering it the same way they enter any other level.

In the SNES game, punching a Climbing Koopa awarded 100 points. In the Game Boy Advance game, this was changed to 400 points.

Points awarded in the SNES game are lower than the Game Boy Advance game for defeating Charging Chuck. Also, in the Game Boy Advance game, coins are awarded for defeating Charging Chuck with fireballs.

Yoshi turns into Blue Yoshi if he has wings when a level is completed in the SNES game. In the Game Boy Advance game, Yoshi will not change into Blue Yoshi if he has wings when completing a level.

Yoshi can spit the key out after entering a keyhole in the SNES game. This was removed from the Game Boy Advance game.

In the SNES game, Mario and Luigi can not spin jump on some enemies that they can in the Game Boy Advance game, such as Boos and Podoboos. Also, in the Game Boy Advance game, Yoshi can jump off of fish enemies.

By holding the run button, Mario and Luigi can climb vines faster in the Game Boy Advance game.

In the SNES game, Yoshi will always produce an egg containing a mushroom when he eats ten red berries. In the Game Boy Advance version Green Yoshi will produce an egg with a mushroom, Blue Yoshi will produce an egg with a feather, Red Yoshi will produce an egg with a Fire Flower, and Yellow Yoshi will produce and egg with a Starman.

In the SNES game, Yoshi has orange arms regardless of his body color, though he has green arms on the SNES box art. In the Game Boy Advance version, Yoshi's arms are the same color as his body.

In the SNES game, player 1 controls Mario and player 2 controls Luigi. In the Game Boy Advance game, the player can choose to play as either Mario or Luigi by pressing the R button on the world map. Additionally, in the SNES version Luigi is an exact copy of Mario with a different color palette. In the Game Boy Advance version, Luigi was changed in several ways including:
• Luigi is taller and skinnier than Mario and more closely resembles his modern apperance. Luigi also wears blue overalls instead of his purple overalls from the SNES version.
• Luigi jumps higher, moves slower, and scuttles in mid-air much like he does in Super Mario Bros. 2 (U.S. version). He also runs slower and has worse traction than Mario.
• Luigi flies higher with his cape than Mario, but also flies slower.
• Fireballs from Fire Luigi bounce higher.
• When Luigi rides Yoshi, Yoshi doesn't instantly eat enemies; Yoshi can spit enemies out, and use some of them as weapons, but swallows them after 7-8 seconds.
• All coins will fall out of a block if Luigi hits it, whereas the coins come out one-by-one when Mario hits the same block.

In the Game Boy Advance game, earning at least 10 lives consecutively will cause a flower and the number of lives earned to scroll across the screen.

In the SNES game, the player can only save after completing certain stages or finishing any Ghost House or Fortress. In the Game Boy Advance game, the player can save inside of a course or on the world map; the Game Boy Advance game also saves the player's power-ups and life count, whereas the SNES version starts the player out as Small Mario with 5 lives each time a saved file is loaded.