The clinical neurophysiological tests allow us to determine the type, extent, and nature of brachial plexus damage. They are crucial in decision making regarding surgical procedures or conservative treatment. This report aimed to present an algorithm for rehabilitation procedures in patients with brachial plexus injury of various origins based on the results of neurophysiology findings for the selection of procedures supporting the process of nerve and muscle regeneration. The research group consisted of patients whose medical documentation was analysed concerning the reason, level, and localization of damage to the brachial plexus structures, surgical and or rehabilitative treatment, as well as the MRI results. Among the group of fourteen patients, the clinical studies showed the greatest incidence of brachial plexus injuries of the mixed (both pre- and postganglionic), all trunks, and cervical root injuries, respectively. Results of the motor evoked potentials (MEP) and electroneurography (ENG) recordings induced at levels of spinal roots and Erb’s point showed a decrease of more than 40% in amplitudes on the symptomatic side in comparison to the asymptomatic side. This diffeence was recorded for the axillary and radial innervation and the C5, C6, and C7 root domains, ranging from 57% to 66%; the lowest decrease was recorded following electrical stimulation at Erb’s point for the ulnar nerve (34%). The latency prolongation on the symptomatic side in CMAP and MEP tests ranged from 0.2 to 1.7 ms, with the most following magnetic stimulation of the C5 cervical root for the axillary innervation. Most of the results indicated the axonotmesis and neuropraxia type of injury in motor fibers (40%) confirmed by EMG results. The sensory conduction studies (SNCS) in distal nerve branches did not confirm the severe advancement of the brachial plexus injury (63%). The proposed algorithm of the physiotherapeutic procedures should be mainly targeted for recovery of motor dysfunction as the consequence of brachial plexus injury. Rehabilitation should incorporate the treatment supporting nerve regeneration, muscle strengthening, and maintaining functional ranges of motion of the injured extremities. The rehabilitation treatment for patients with brachial plexus injuries is an individualised process, and the selection of procedures and the effectiveness of the treatment undertaken should be confronted with results of neurophysiological tests verifying the motor neural transmission from the level of the cervical motor centre to the effector, peripheral nerve function, and muscle’s motor unit activity.