SkyGunner is a 3rd person flight combat game, with its emphasis on action. Players choose to take the role of either Ciel, Copain or Femme, each with their own campaign and unique flying abilities and special skill. Players can turn the plane's direction up, down, left and right, perform barrel rolls, use afterburners and breaking. Weaponry is handled by a complex system of targeting, with involves two types: "Look Targeting" and "Weapon Lock". Look Targeting simply assigns a particular enemy as the center of the camera and can be switched between at any time. The player must still maneuver near the enemy and target them with the cross hairs in order to fire on them. Depending on the secondary weapon selected, players can roll the cross hairs over the wing leader of an enemy group or the sequentially lead gun on a battleship, allowing the player to instantly target multiples from that group.

The primary weapon of each airplane is a machine gun which fires straight ahead. More destructive secondary weapons are also available, and include Fireworks Missiles which create area explosions, Dog Missiles which slow and/or immobilize targets and Cross Missiles which stick to targets and need to be shot by a machine gun to detonate. Copain also has his own weapon, the Pumpkin Bomb which is a big destructive bomb. These secondary weapons are automatically replenished with the destruction of chains of enemies and/or combos. Chains/Combos are also the way to activate score multipliers, which affect the amount of money won in each mission. Ciel, Copain and Femme are continually in competition throughout the game and often bonuses (such as faster engines) are given to the character with the highest score in specific missions. Bonus scores are also awarded for specific mission events.