In Trap Gunner two opponents battle in small arenas, and while each has a relatively weak ranged and melee attack, the favored means of damaging an opponent is through hidden traps. Each combatant has at his or her disposal a range of explosives, pits, throwing panels, and gas bombs. An enemy is significantly damaged by a single trap, but one may create a sequence of traps for a devastating amount of damage.

With one of six different special agents, each a specialist in assassination and demolitions, a player may progress through a story mode consisting of several missions, a sub-boss, and a final boss. These characters are also available for custom battles against a human or the computer.