A belt drive system by a toothed belt, transmits energy between gears, and controls the rotary angle of the load by the torque from a drive motor. The purpose of this research is to develop an appropriate control method about factors of deteriorating the control performance in the tracking control of the belt drive system. Backlash is an element caused by the gap of the meshing of the gear, and a delay occurs in the load side. Therefore, the backlash is considered as the deteriorating factor. Another one is the uncertainty that exists in the dynamics of the system. By such deteriorating factors, the positioning accuracy is deteriorated, and it may cause the limit cycle, the steady-state error, the response delay and instability. In this paper, a design method of the tracking control system is proposed for the belt drive system in which backlash and characteristic uncertainties exist simultaneously. The influence of the backlash is suppressed, which is the nonlinear element regarded as a disturbance of the linear system. A control system that guarantees robust stability with respect to uncertainty is designed based on the robust control theory. Experiments show that the effectiveness of the proposed method comparing with other conventional control system design methods.