Acceleration control using a disturbance observer is a strategy of robust motion control. In the acceleration control, fast sampling rate is a key issue to improve the performance of robustness. By using FPGAs, faster sampling rates can be achieved than those using PCs. The sampling rates of the systems using FPGAs can be faster than the frequency of PWM wave. In that case, the performance of the acceleration control is not improved as expected. The frequency of the PWM wave becomes a performance limitation of the system. In this paper, a position control system based on acceleration control using multirate sampling method is implemented into an FPGA to overcome the limitations. In these multirate systems, the sampling rates of the system output and control calculations are faster than that of the system input. Experimental results show that the robustness of the system can be improved, even though the sampling rates of the system output and the control calculations are faster than the PWM frequency by using the multirate sampling method.