A position controller which can achieve a specified dynamic performance irrespective of the different operating position of the pneumatic cylinder is proposed. The position controller developed in this paper is composed of a nonlinear compensator and a disturbance observer. The nonlinear compensator which feeds back position, velocity and acceleration is derived from the nonlinear dominating equations of the position control system to compensate for variation of dynamic characteristics of a pneumatic cylinder according to the change of the operating position. The disturbance observer including a simplified linear model is designed to reduce the effect of model discrepancy in the low frequency range which cannot be suppressed by the nonlinear compensator. The results of the experiments show that the position control performance maintains a designed performance regardless of the variations of an operating position of the pneumatic cylinder.