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Functional electrical stimulation (FES) of pedaling provides a means by which individuals with spinal cord injury can obtain cardiorespiratory exercise. However, the early onset of muscle fatigue is a limiting factor in the cardiorespiratory exercise obtained while pedaling an FES ergometer. One objective of this study was to determine muscle excitation timing patterns to increase muscle endurance in FES pedaling for three upper leg muscle groups and to compare these timing patterns to those used in a commercially available FES ergometer. The second objective was to determine excitation timing patterns for a lower leg muscle group in conjunction with the three upper leg muscle groups. The final objective was to determine the mechanical energy contributions of each of the muscle groups to drive the crank. To fulfill these objectives, we developed a forward dynamic simulation of FES pedaling to determine electrical stimulation on and off times that minimize the muscle stress-time integral of the stimulated muscles. The computed electrical stimulation on and off times differed from those utilized by a commercially available FES ergometer and resulted in 17% and 11% decrease in the muscle stress-time integral for the three upper leg muscle groups and four upper and lower leg muscle groups, respectively. Also, the duration of muscle activation by the hamstrings increased by 5% over a crank cycle for the computed stimulation on and off times, and the mechanical energy generated by the hamstrings increased by 20%. The lower leg muscle group did not generate sufficient mechanical energy to reduce the energy contributions of the upper leg muscle groups. The computed stimulation on and off times could prolong FES pedaling, and thereby provide improved cardiorespiratory and muscle training outcomes for individuals with spinal cord injury. Including the lower leg muscle group in FES pedaling could increase cardiorespiratory demand while not affecting the endurance of the muscle- - s involved in the pedaling task.