Thunder Force II is both a side scrolling and top down shooter. In the game you control a ship. In some stages the action is side scrolling and in others it is top down (overhead). The weapons systems is fairly basic. You can switch from shooting a more powerful weapon straight ahead or two less powerful guns shooting forward and backward simultaneously. There are various power-ups that improve your fire power.

In the top down levels you can only travel in cardinal directions and cannot maneuver around obstacles easily or slow down. The control in the side scrolling levels is reminiscent of R-Type or Gradius, but with more basic weapons systems. In future incarnations of the series the top down aspect would be abandoned.