Gameplay in Metal Slug Advance is very similar to any other Metal Slug game. Two new systems, the life system and the card system, are present in this game.

The life system is simply a life bar for the players, as it replaces the extra lives and credits from all the other Metal Slug games. As players take damage, the life bar depletes (different attacks cause different amounts of damage). Collecting food items restore health. Players instantly die from being crushed or falling down a pit. Dying places the player to a previous checkpoint rather than on the spot, and any prisoners rescued and cards collected are lost.

The card system is the collection aspect of the game. There are 100 cards to collect. Cards can be found from shooting certain parts of the background, obtaining it from certain hostages, and sometimes by doing both. The cards have many different purposes, from giving detailed info on items and characters from the Metal Slug series, boosting player abilities, and even unlocking Slugs.

Metal Slug Advance has five missions. The first four are straightforward while the Final Mission has multiple routes. Collecting a special card in the Final Mission unlocks the Dungeon, a maze-like cave where twenty-five prisoners are present and certain cards clear once blocked paths in Mission 1 and Mission 3.

All weapons bar the Two Machine Guns return in this game albeit with their weapon ammo reduced in half. Collecting the respective weapon clip card will increase ammo count to its original amount.