Cycling induced by automatic control of functional electrical stimulation provides a means of therapeutic exercise and functional restoration for people affected by paralysis. During cycling induced by functional electrical stimulation, various muscle groups are stimulated according to the cycle crank angle; however, because of kinematic constraints on the cycle-rider system, stimulation is typically only applied in a subsection of the crank cycle. Therefore, these systems can be considered as switched control systems with autonomous, state-dependent switching with potentially unstable modes. Previous studies have included an electric motor in the system to provide additional control authority, but no studies have considered the effects of switched control in the stability analysis of the motorized functional electrical stimulation cycling system. In this paper, a model of the motorized cycle-rider system with functional electrical stimulation is developed that includes the effects of a switched control input. A novel switching strategy for the electric motor is designed to only provide assistance in the regions of the crank cycle where the kinematic effectiveness of the rider's muscles is low. A switched sliding-mode controller is designed, and global, exponentially stable tracking of a desired crank trajectory is guaranteed via Lyapunov methods for switched systems, despite parametric uncertainty in the nonlinear model and unknown, time-varying disturbances. Experimental results from five able-bodied, passive riders are presented to validate the control design, and the developed control system achieves an average cadence tracking error of revolutions per minute for a desired trajectory of 50 revolutions per minute. Note to Practitioners-Autonomous systems designed for rehabilitation and functional assistance for people with disabilities such as paralysis have the potential to maximize rehabilitative outcomes and improve the quality of life for millions of people. Disorders such as paralysis drastically reduce a person's ability to complete tasks due to a loss of neuromuscular control. Functional electrical stimulation can activate paralyzed muscles, restoring functional ability through automated application of electric current to the neuromuscular system, and, when applied to a task such as cycling, is both rehabilitative and empowering. However, cycling induced by functional electrical stimulation is limited by the capability of the rider's muscles, so an electric motor is typically added to accommodate the rider's ability and to support stability. The response by muscle to electrical stimulation is uncertain, time-varying, and nonlinear, and switching the control input across multiple muscle groups and between the rider and an electric motor make guaranteeing stability and performance challenging. This paper presents a novel approach to the challenge of controlling motorized cycling systems with functional electrical stimulation that considers the switching effects and guarantees exponentially stable tracking of a desired crank trajectory, and experimental results indicate how the control system may be applied to a rehabilitative cycling task. Directions for future research are aimed at implementation of the developed control system in patient populations with paralysis to quantify its impact on therapeutic outcomes such as muscle function and neuroplasticity.