In patients with global brachial plexus injury and lack of biological treatment alternatives, bionic reconstruction, including the elective amputation of the functionless hand and its replacement with a prosthesis, has recently been described. Optimal prosthetic function depends on a structured rehabilitation protocol, as residual muscle activity in a patient’s arm is later translated into prosthetic function. Surface electromyographic (sEMG) biofeedback has been used during rehabilitation after stroke, but has so far not been used in patients with complex peripheral nerve injuries. Here, we present our rehabilitation protocol implemented in patients with global brachial plexus injuries suitable for bionic reconstruction, starting from the identification of sEMG signals to final EMG electrode placement within a prosthetic socket. This structured rehabilitation program facilitates motor relearning, which may be a cognitively debilitating process after complex nerve root avulsion injuries, aberrant re-innervation and extra-anatomical reconstruction (as is the case with nerve transfer surgery). The rehabilitation protocol using sEMG biofeedback aids in the establishment of new motor patterns as patients are being made aware of the advancing re-innervation process of target muscles. Additionally, faint signals may also be trained and improved using sEMG biofeedback, rendering a clinically "useless" muscle (exhibiting muscle strength M1 on the British Medical Research Council [BMRC] scale) eligible for dexterous prosthetic hand control. Furthermore, functional outcome scores after successful bionic reconstruction are presented in this article.