This flight simulator simulates a real aircraft, the Piper PA-28-181 Archer II. For those with the knowledge, it offers practice with the variables of flight, including the avionics. The Atari ST and Amiga releases instead simulate the Cessna 182RG single engine propeller aircraft and the Gates Learjet 25G twin engine jet.

The game has more features than first generation flight simulators. Pilots are expected to pay attention to small details. SubLOGIC encouraged the players to go to flight stores and purchase flight-training manuals and aeronautical charts to help them understand the variables within the program. The game is oriented toward pilots-in-training, but there are options for laymen too: an easy mode, and a slightly more detailed reality mode. These modes do not require the same level of knowledge.

Flight Simulator II is packaged with a WWI dogfighting game, called WWI Ace. In this game the plane is armed with bombs, machine guns, and a radar screen. The radar screen is anachronistic for a game set in World War I, but it is there to make the gameplay easier.