The goal of this paper is to control the trajectory of the flight path of six degree of freedom flying body model using Fractional PID controller (FPID) and Gain Schedule Fractional PID controller. FPID and gain schedule FPID controllers gains with non linear flying body simulation are tuned by Simulink design optimization. Gain Schedule FPID controller is able to compensate for constraints that represent physical limits of actuators in pitch angle. The gain schedule FPID for the six degree of freedom flying body is designed in two phases. The first phase is boost phase where the thrust force is maximized. The second phase is sustain phase where the thrust force is minimized. The results of gain schedule FPID controller are compared with the results of FPID controller.