In this paper, a tracking control technique developed for the control of nonminimum phase systems has been applied to the autopilot design of a tail-controlled skid-to-turn(STT) missile system. The inversion-based control can not be directly applied to nonminimum phase system due to unstable zero dynamics. But output-redefinition method gives the indirect way to apply the inversion-based control to nonminimum phase systems. The robustness problems of the inversion-based control against uncertain system parameters are briefly investigated and a robust plant inversion by robust eigenstructure assignment is suggested. Robust performance is enhanced by making the zero dynamics robust to the parameter perturbations. Also an auxiliary robust control loop using classical proportional-integral-derivative error feedback controller is used. The results are verified through numerical simulation.