The purpose of this work is to develop the FES controller that can cope with the muscle fatigue which is one of the most important problems of current FES (Functional Electrical Stimulation). The feasibility of the proposed FES controller was evaluated by simulation. We used a fitness function to describe the effect of muscle fatigue and recovery process. The FES control system was developed based on the biological neuronal system. Specifically, we used PD (Proportional and Derivative) and GC (Gravity Compensation) control, which was described by the neuronal feedback structure. It was possible to control of multiple joints and muscles by using the phase-based PD and GC control method and the static optimization. As a result, the proposed FES control system could maintain the cycling motion in spite of the muscle fatigue. It is expected that the proposed FES controller will play an important role in the rehabilitation of SCI patient.