Raiden Fighters Jet's stage branching mechanic is explained in the game as being part of a training simulation that gauges the player's performance in the simulation. Players who perform well in the simulation will get a chance to pilot a new experimental fighter in a real mission. Depending on the player's performance in the real mission, they will be either given the chance to fight a bomber carrying a nuclear cruise missile or be forced to withdraw before engaging it.

A mechanic introduced in this game gauges stage progression on player performance. If the player performs well in a stage, the next stage will have a higher level number, allowing the player to reach the real levels (Phase 1 and Phase 2) earlier. Players not performing well will be sent to a lower level number, or the game session ends early. Additional game modes include playing through all boss encounters only, and a mode in which enemies return fire after being destroyed.

Controls consist of an 8-way joystick to manoeuvre and 2 buttons to drop bombs and shoot bullets at your enemies. A number of power-ups are dropped by enemies throughout the game to give you an advantage.