Raiden Fighters 2 has simplistic controls typical of shooting games. A fire button fires the player's weapons. A Bomb button triggers a special attack that damages enemies and cancels enemy fire on a large area.

A new feature introduced in Raiden Fighters 2 is the hybrid attack, available only in a two-player game. When two players are close to each other and use their loaded attacks, the hybrid attack is activated, making them invincible for the duration of the attack.

Medals appear more often than in the first game, giving players more scoring opportunities.