An aircraft security system comprises a transparent bullet-proof security chamber interposed between the pilot area and the passenger area, and providing the only means of passage to the pilot area. The security chamber has a cockpit door to the cockpit area and passenger door to the passenger area. The passenger door must be closed when the cockpit door is open and vice versa. A third, or entry door, may be used to facilitate boarding the aircraft. All doors are closed and locked when sensors indicate unauthorized entry of a passenger into the security chamber.