In this paper, a fully automatic robust control strategy is proposed for control of paraplegic pedaling using functional electrical stimulation (FES). The method is based on higher-order sliding mode (HOSM) control and fuzzy logic control. In FES, the strength of muscle contraction can be altered either by varying the pulse width (PW) or by the pulse amplitude (PA) of the stimulation signal. The proposed control strategy regulates simultaneously both PA and PW (i.e., PA/PW modulation). A HOSM controller is designed for regulating the PW and a fuzzy logic controller for the PA. The proposed control scheme is free-model and does not require any offline training phase and subject-specific information. Simulation studies on a virtual patient and experiments on three paraplegic subjects demonstrate good tracking performance and robustness of the proposed control strategy against muscle fatigue and external disturbances during FES-induced pedaling. The results of simulation studies show that the power and cadence tracking errors are 5.4% and 4.8%, respectively. The experimental results indicate that the proposed controller can improve pedaling system efficacy and increase the endurance of FES pedaling. The average of power tracking error over three paraplegic subjects is using PA/PW modulation, while the tracking error is when PW modulation is used. The subjects could pedal for 15 min with about 4.1% power loss at the end of experiment using proposed control strategy, while the power loss is 14.3% using PW modulation. The controller could adjust the stimulation intensity to compensate the muscle fatigue during long period of FES pedaling.