Gameplay in Cannon Fodder revolves around guiding a team of up to six soldiers through 72 levels of combat, with objectives varying between each mission. The game combines action and strategy elements, as players control their soldiers indirectly using the mouse or joypad. By highlighting and clicking on certain buttons, troops can be moved to specific spots and fired at enemies. Players can also pick up grenades or rockets, which can be used to destroy groups of enemies, buildings, or vehicles.
One of the unique features of Cannon Fodder is the use of terrain and environment to gain an advantage over the enemy. Water cannot be shot within, so finding and controlling bridges becomes crucial. The arrangement of trees can provide hiding places to shoot from, but CPU soldiers will also be using these spots. Players must utilize this information strategically to succeed in each mission.