Gameplay is similar to the Wii U version. However, some items have been replaced or are not available, there are 100 courses designed by Nintendo that come pre-installed and any courses created by the player cannot be uploaded online and can only be shared via local multiplayer.
Differences from the Wii U version
- There is no Mystery Mushroom. It has been replaced by the Weird Mushroom.
- A minigame called Gnat Attack has been added.
- Items such as Checkpoint Flags, Skewers and Keys are available without shaking an arrow sign.
- The Super Mario Bros. 3 and Super Mario World game styles are available at the beginning of the game.
- Players can collaborate on a course via Local Play
- The Nintendo 3DS version does not support amiibo functionality.
- There is a Data Reset glitch which doesn't happen on the Wii U.
- To make the glitch work, If one Cartridge of Super Mario Maker 3DS has progressed on the homing 3DS, insert it into another 3DS and play it on that 3DS. Give back the Cartridge to the original 3DS and there all of the progress will be gone.
- This doesn't happen in the Wii U version, but there will be new progress once the disk is put onto another Wii U Console.