Movement disabilities due to spinal cord injury (SCI) are usually incomplete, leaving the patients with partially functioning movement system. As a result, functional electrical stimulation (FES) systems for restoration of movement to the paralyzed limbs must operate in parallel with the residual voluntary movements of the patient. In the resulting man-machine system, the central nervous system (CNS) controls the residual voluntary movements while the FES system controls the paralyzed muscles of the same limbs. Clearly, these two control systems must work in synchrony to benefit the patient. In this chapter we will discuss different methods for cooperative control of man-machine FES systems and use a clinical FES system to demonstrate the successful application of these strategies.