Flight Management Systems (FMS) in today’s airplanes help the pilot in guidance, control and handling flight plans based on standard tables and performance monitoring in order to reduce the pilot work load during flight. Despite great advances, modern avionics, regular checks and using multiple redundancies in vital systems, the possibility of fault or failure occurrence still exist. Considering the changes in airplane in emergency conditions and pilot challenges for fast decision making and choosing a safe landing site, the FMS must enhance to help the pilot in emergency conditions. Accordingly, the emergency FMS is introduced in this paper to cover the pilots’ challenges in emergency, effective communication between the pilot and the automatic system and therefore to improve the flight safety. The proposed FMS include different parts and subsystems like identification, structural health monitoring, controller, trajectory generation, environment database, flight envelope, pilot interface; etc. in addition, a novel landing site selection algorithm and a pilot interface are introduced as an inevitable subsystems in emergency flight management system.