Nerve-transfer surgery is the treatment of choice for traumatic brachial plexus injuries (tBPIs). Combined electromyography (EMG) follow-ups and results obtained by transcranial magnetic stimulation (TMS) may provide useful follow-up of rehabilitation outcomes of elbow flexion in C5-C7 tBPIs. A total of 11 patients with complex tBPIs, operated by the Oberlin surgical technique, were assessed clinically (British Medical Research Council’s score—MRC) and by EMG + TMS after undergoing neuromuscular electrical stimulation and proprioceptive neuromuscular facilitation. Dynamometer quantitative muscle strength (DQMS) was also assessed for overall grip strength evaluation. Six patients continued rehabilitation three times a week, whereas five patients did not follow recommendations for continuous physical therapy (PT). All patients were assessed after 6 months as planned. Following a 6-month PT protocol, clinical improvements correlated with decreases of the Motor Evoked Potential (MEP) latency recorded at the first dorsal interosseous muscle, biceps brachii, and cortical level in the sublot group with continuous PT protocol compliance. We obtained significant amelioration of MEP latency and needle EMG signs of amelioration in these six patients. These cases also correlated to the MRC improvement in elbow flexion, as well as DQMS parameters. TMS parameters also mildly and inconstantly improved in the other five patients who limited themselves just to PT after surgery; however, there was no correlation with the EMG findings or MRC scaling. PT influences the cortical representation within the motor area of the upper limb when performed continuously. The electrical signals within the motor cortex promote the utility adherence to long-term PT protocols.