In 2003, the fourth and final entry in the Super Mario Advance series, Super Mario Advance 4: Super Mario Bros. 3 was released for the Game Boy Advance. It was actually a heavily updated version of Super Mario Bros. 3 as the name suggests. However, it boasted similar graphics and sound to the All-Stars version. It features a save system similar to the Super Mario All-Stars save system, except temporary saves may now be done anywhere.

This game's largest added feature was compatibility with the e-Reader and e-Cards. These cards could be scanned in to the game, and would function as new levels, instant power-ups, or demos. One power-up card features a power-up that cannot be found in any other Mario game: the Boomerang.

Some changes were:

The 1 Player and 2 Player options were replaced with the option as playing as either Mario or Mario & Luigi, which is essentially identical to the former options. Luigi's animations are similar to his Super Mario All-Stars: Super Mario Bros. 3 counterpart, but he now has his Super Mario Bros. 2-styled "Flutter Jump", i.e. he can stay in the air a bit longer than Mario. Spade Panels now produce different variants in response to completing one. It goes from Spade > Heart > Club > Diamond Mario can have more than 100 lives. Getting a Fire Flower or Raccoon Leaf will have their usual effect rather in the situation of Mario taking damage to revert to small Mario before he touches the power-up; previously this would just have the effect of a Mushroom. Koopa Troopas can now be stomped underwater. Giant Brick Blocks can now be broken with Mario's tail (with the Raccoon or Tanooki suit). In several levels of World 4, just before the Goal Panel, there is a coin bonus in the sky. In World 5, some brick blocks that otherwise make Pipes and Bullet Bill cannons float in the air contain coins. In World 6, the path to the Mushroom House was altered so the player does not have to do 6-5 to access it. A few sprites were slightly improved. For example Mario and Luigi now wear their gloves. Previous versions had the two gloveless, the NES version due to color limitations and the All-Stars version for unknown reasons. Mario can carry shells into pipes without losing them. The player can now slope slide as Hammer Mario.