The goal is to control the trajectory of the flight path of six degree of freedom flying body model using fractional PID. The design of fractional PID controller for the six degree of freedom flying body is described. The parameters of fractional PID controller are optimized by particle swarm optimization (PSO) method. In the optimization process, various objective functions were considered and investigated to reflect both improved dynamics of the missile system and reduced chattering in the control signal of the controller.