Different combinations of stimulation frequency and intensity can generate a targeted force during functional electrical stimulation (FES). This study compared isometric performance and muscle fatigue during repetitive stimulation with three different combinations of frequency and pulse duration that produced the same initial peak forces: protocol 1 used long pulse duration (fixed at 600 μs) and 11.5 ± 1.2 Hz (low frequency); protocol 2 used 30 Hz (medium frequency) and medium pulse duration (150 ± 21 μs); and protocol 3 used 60 Hz (high frequency) and short pulse duration (131 ± 24 μs). Twenty and 60 Hz pre- and postfatigue testing trains were delivered at the pulse duration used by the fatiguing trains and at 600 μs pulse duration. The percentage decline in peak force between the first and last fatiguing train of each protocol was the measure of muscle performance. The declines in peak force of the 60 Hz testing trains were used to measure muscle fatigue. The 20 Hz:60 Hz peak force ratio was used as a measure of low-frequency fatigue. The results showed that protocol 1 produced the least decline in peak force in response to the fatiguing trains, as well as the least muscle fatigue and low-frequency fatigue when the pulse duration was maintained at the level used by the fatiguing trains. Interestingly, protocol 2 produced the least muscle fatigue, and there were no differences in the levels of low-frequency fatigue across protocols when a comparable motor unit population was tested using 600 μs pulse duration. The results suggest that if the frequency and intensity are kept constant during FES, using the lowest frequency and longest pulse duration may maximize performance.