Functional electrical stimulation (FES) systems have been developed to help restore various neuromuscular functions in individuals with neurological disorders leading to paralysis. Most of the current FES systems are designed for specific neuroprosthesis applications (i.e., walking, grasping, bladder voiding, coughing, etc.) and when one intends to use them in other custom made applications they are very limited due to a lack of functionality and flexibility in hardware and programmability. This prevents effective and efficient development of customized neuroprostheses. Research and development efforts at the Rehabilitation Engineering Laboratory at the University of Toronto were being carried out with an objective to produce a new, fully programmable and portable FES system. This thesis presents a novel proof-of-concept prototype controller for use in the new FES system. The controller subsystem manages and controls the overall FES system including the real-time decoding and execution of stimulation, data acquisition, external systems interfaces and user interface.