A method of treating shoulder dysfunction involves the use of a percutaneous, intramuscular stimulation system. A plurality of intramuscular stimulation electrodes are implanted directly into select shoulder muscles of a patient who has suffered a disruption of the central nervous system such as a stroke, traumatic brain injury, spinal cord injury or cerebral palsy. An external microprocessor based multi-channel stimulation pulse train generator is used for generating select electrical stimulation pulse train signals. A plurality of insulated electrode leads percutaneously, electrically interconnect the plurality of intramuscular stimulation electrodes to the external stimulation pulse train generator, respectively. Stimulation pulse train parameters for each of the stimulation pulse train output channels are selected independently of the other channels. The shoulder is evaluated for subluxation in more than one dimension. More than one muscle or muscle group is simultaneously subjected to a pulse train dosage. Preferably, the at least two dosages are delivered asynchronously to two muscle groups comprising the supraspinatus in combination with the middle deltoid, and the trapezious in combination with the posterior deltoid.