In this study, position and force simultaneous trajectory tracking control apparatus with pneumatic cylinder driving system is proposed. The pneumatic cylinder driving system that consists of two pneumatic cylinders constrained in series and two proportional flow control valves offers a considerable advantage as to non-interaction of the actuators because of the low stiffness of the pneumatic actuators. The controller applied to the driving system is composed of a non-interaction controller to compensate for interaction of two cylinders and a disturbance observer to reduce the effect of model discrepancy of the driving system in the low frequency range that cannot be suppressed by the non-interaction controller. The experimental results with the proposed control apparatus show that the interacting effects of two cylinders are eliminated remarkably and the proposed control apparatus tracks the given position and force trajectory accurately.