Alien Hominid is a side-scrolling shooter in a similar vein to games such as Metal Slug, where one hit instantly kills and has a two-player simultaneous play. Players take over as the titular hominid, who has to fend off waves of secret agents. His main arsenal is a blaster, while players can also melee close-up enemies and use a limited number of grenades to attack. Advanced moves include rolling under shots, jumping on and biting off enemies' heads, temporarily scaring other enemies, and digging underground to drag enemies down with them.

Players can collect a numerous variety of power-ups which simultaneously give players extra grenades, a shield, and unique ammo. Players can also drive vehicles, ride on top of a Yeti, and pilot a UFO. Completing certain tasks will unlock hats the players can dress their Hominid in. The main game features sixteen stages.

Outside of the main game, there are three multiplayer modes (Challenge, Neutron Ball, and Pinata Boss), a PDA game (featuring around 200 levels and a level editor), an extra mode called All You Can Eat, and a retro minigame, Super Soviet Missile Mastar.