Functional electrical stimulation (FES) has been adopted to provoke muscle contraction and promote the execution of exercises by individuals with spinal cord injury (SCI). Several benefits are observed in the application of this technique, such as improvement in cardiovascular function, increase in muscle mass, reduction in bone mass loss, and improvement in metabolism. However, due to the complexity of these systems it can be quite complicated for therapists and people with SCI to use FES. Another major limitation for these systems is the lack of modularity and flexibility in changing or adding features, such as sensors and stimulators. This paper presents a modular and flexible system for functional electrical stimulation cycling that has a portable graphical control interface to manage the system.