Functional electrical stimulation (FES) of paralyzed muscles holds promise as a strategy to assist patients in executing functional movements after spinal cord injuries. Muscle atrophy is one of the major problems that must be addressed for this approach to be successful. Loss of muscle mass may occur as a result of lesions to motoneurons in either the spinal cord or the central command pathway, or a combination of the two. For injuries to spinal motoneurons, muscle fibers undergo denervation atrophy. Damage to the central command pathway, on the other hand, results in disuse atrophy. In association with atrophy, the low contractile forces and inability of the muscles to sustain contractions are of direct therapeutic concern. In this review, methods aimed at recovery of function of paralyzed limbs by reducing susceptibility to fatigue and atrophy of paralyzed muscles are discussed. One is related to promoting nerve sprouting in partially denervated muscles to reinnervate muscle fibers and reverse denervation atrophy. The other regards training of paralyzed muscles to increase strength (muscle force) and endurance (fatigue resistance) by means of FES. Most training regimens with low-frequency FES increase muscle endurance. Efforts to design optimal regimens for increasing both muscle strength and endurance must involve consideration of several factors that are still controversial. These factors, which include muscle properties (such as fiber type composition and physiological type) and conditions imposed on the muscle (such as loading) during contractions elicited by FES, are discussed in detail.