Estimation of the correct motion intention of the user is very important for most of the Electromyography (EMG) based control applications such as prosthetics, power-assist exoskeletons, rehabilitation and teleoperation robots. On the other hand, safety and long term reliability are also vital for those applications, as they interact with human users. By considering these requirements, many EMG-based control applications have been proposed and developed. However, there are still many challenges to be addressed in the case of EMG based control systems. One of the challenges that had not been considered in such EMG-based control in common is the muscle fatigue. The muscle fatiguing effects of the user can deteriorate the effectiveness of the EMG-based control in the long run, which makes the EMG-based control to produce less accurate results. Therefore, in this study we attempted to develop a fuzzy rule based scheme to compensate the effects of muscle fatigues on EMG based control. Fuzzy rule based weights have been estimated based on time and frequency domain features of the EMG signals. Eventually, these weights have been used to modify the controller output according with the muscle fatigue condition in the muscles. The effectiveness of the proposed method has been evaluated by experiments.