A checkpoint is a level retry gimmick found in many platforming games and with Mushroom Kingdom Fusion being no exception. Clearing a checkpoint allows the player to restart the level from that point instead having to restart the level from the very beginning should he or she fail to clear the stage. Checkpoints are usually found in the middle of a level and some levels have more than one checkpoint likely due to the longer length of the level. Some levels don't feature checkpoints at all due to their short length. A level's checkpoint is reset if the player chooses to enter another level instead.
The checkpoint's appearance is determined by the level or world theme:
- World 1 - The Midway Gates from Super Mario World.
- World 2 - Flags from Metal Slug.
- World 3 - Small flagpole with Mega Man's face on it from the Mega Man games.
- World 4 - Skull switches from the Doom series. The sound they make when activated comes from Quake.
- World 5 - Crystal-shaped checkpoints, based on the crystal enemies from Kid Chameleon.
- World 6 - Owl Statues from the Zelda series, specifically the one based on Majora's Mask.
- World 7 - Star Posts from the Sonic series.
- World 8 - Small Post with a Yellow star from Kirby: Canvas Curse.
- World 9 - Safe Screens from 1993 video game Alien Carnage.
- World 0 - ???
Not every level in a specific world uses the same checkpoint. For example, the few levels in World 2, like N.Sanity Island use a crate-based checkpoint as it is based on the Crash Bandicoot series, where as most of the levels in World 2 use the Metal Slug flags.