The gameplay is typical of the sidescrolling, platform games of the era. The player controls Colonel Jack O’Neill and navigates him through the various locations by walking/running, jumping and climbing. O’Neill's health is indicated by an energy bar found alongside information such as weapon status and grenade count on the heads-up display. Most missions consist of finding people or items in one of several different locations. There are two missions that involve flying one of Ra's gliders and partaking in dogfight style combat. The radio screen displays the player's current mission, as well as other information such as the number of lives, continues, hieroglyphs, bomb pieces, and current password.

There are many different enemies through the game, ranging from minor inconveniences like the fleeting scarab beetles to the difficult Horus guards. There are three boss encounters; Anubis twice, and the final confrontation with Ra. If the player has not collected all seven bomb pieces and all seven hieroglyphs by end of the game, they will lose the game, even if they defeat Ra.

The player is equipped with a single machine gun with infinite ammunition that can be temporarily upgraded with pickup items such as rapid fire, wide fire, ammunition strength, and the gun coolant. The player can also pickup and hold up to 99 standard grenades in addition to the more powerful alien grenades.