Mutant Night is a shoot'em up game of the "run & gun" type : the players controls a walking character shooting at enemies while avoiding their attacks.[4] Unlike most run&gun games, Mutant Night has almost no platform part and the character's shooting power is very limited : short range and not multi-directional, the bubble are always shot in the direction the character is facing.

The game is divided in various levels or acts and focuses on fast-paced action and memorization. The levels are very short and straightforward, with a level design relying only on enemies attack patterns and on the game's physics to challenge the player. Mutron-kun can walk left or right, shoot bubbles and jump, and hurries to reach a small trapdoor at the end of each level. The difficulty curve of the game increases significantly after the first level and can be somewhat unforgiving.

Power ups are available in the form of small pink pods on the ground which when shot release a coloured orb into the air, which can do one of the following: make Mutron-kun very large and invincible for a short period, transform Mutron-kun into multiple creatures, award extra points or grant increased fire power in a scatter shot pattern.