Behind Enemy Lines is a first person rail shooter where the player controls a machine gun mounted on a jeep driving through enemy territory. The game consists of four missions that all involve infiltrating and destroying various enemy facilities. The setting is modern and enemies include simple foot soldiers, light vehicles such as Jeeps, Humvees, and heavy vehicles like tanks and helicopters.

As in other rail shooters, the player's control is limited to moving a crosshair and shooting, while movement is automatic. The main weapon is a machine gun that can fire both bullets and missiles. There is no reloading, and it's not possible to run out of ammo completely but if the ammo counter gets too low the firing rate will decrease. Therefore, more ammo has to be collected by destroying ammo crates. Missiles, too, have to be collected by destroying crates. They can however only be used on certain heavy targets, such as helicopters and tanks and when aiming on these the missile will automatically lock on the target and the player only has to launch it by pressing the right button. Fuel can also be collected by hitting fuel drums. If the vehicle's fuel supply is depleted the player will get a score penalty.

The game can be played by one or two players each controlling a machine gun.