This paper proposed a robust autopilot design for air to air guided missile and a Hardware-in-the-Loop (HIL) simulation which is based on the derived missile-control transfer functions and the 6DOF simulation model. The introduced autopilot is implemented within the 6DOF simulation to check its robustness against non-modeled dynamics and nonlinearities. The nonlinear 6DOF equations of motions are solved together to obtain the pitch and yaw transfer functions. The missile equations are described in the form of modules programmed within the C++ environments to form the baseline for subsequent design and analysis. Furthermore, a comparison between both our previous work, i.e. classical and robust autopilot, are justified via HIL simulation. The simulation results demonstrated the robustness capability in presence disturbance and noise.