As part of NASA's Mars 2020 rover Mission, an autonomous small-scale helicopter will be sent to Mars to conduct a series of demonstration flights, to validate the feasibility and utility of using helicopters for Mars exploration. In this paper, we present a high-level overview of the flight control system for the Mars Helicopter, including the Guidance, Navigation, and Control subsystems, and the implementation of these on the flight avionics hardware. We also discuss the concept of operations, and the testing, verification, and validation performed in a variety of test venues in preparation for Mars flight.