- Instead of a single menu map, there are two menu maps with both doing different functions. One does sleep mode and allows returning access to the overworld map. The other one allows a use for items and displays the current score for the player.
- The Mini Battle code was changed for this version, due to a lack of the X and Y buttons on the Game Boy Advance. The new code is now holding down SELECT and then pressing L, L, B, A and R in the following order.
- Yoshi only has a limited amount of lives in the very first stage, Welcome to Yoshi's Island!, meaning that the World 0 icon is displayed in the file select.
- A new room has been added in Salvo the Slime's Castle. It is between the second and third rooms in the area.
- More Monkey Madness now has twenty Red Coins.
- An extra Middle Ring had been implented into Marching Milde's Fort.
- The room where Hookbill the Koopa is fought has been redesigned.
- All of the Extra Levels in this game have been remodelled.
- Secret Levels, six in total, are added in the game. They can be unlocked if all of the levels in a world gets a score of 100.
- "Castles - Masterpiece Set" has been renamed to "Ultimate Castle Challenge."
- Most of the SFX has been taken from Yoshi's Story.
- The audio has been downgraded to match the capabilities of the Game Boy Advance.
Alternate title screen
Possibly because the game was rushed, the North American, European and Australian versions of the game's title screen only display the logo without a background.