Targeted Muscle Reinnervation (TMR) improves the biological control interface for myoelectric prostheses after above-elbow amputation. Selective activation of muscle units is made possible by surgically re-routing nerves, yielding a high number of independent myoelectric control signals. However, this intervention requires careful patient selection and specific rehabilitation therapy. Here a rehabilitation protocol is presented for high-level upper limb amputees undergoing TMR, based on an expert Delphi study. Interventions before surgery include detailed patient assessment and general measures for pain control, muscle endurance and strength, balance, and range of motion of the remaining joints. After surgery, additional therapeutic interventions focus on edema control and scar treatment and the selective activation of cortical areas responsible for upper limb control. Following successful reinnervation of target muscles, surface electromyographic (sEMG) biofeedback is used to train the activation of the novel muscular units. Later on, a table-top prosthesis may provide the first experience of prosthetic control. After fitting the actual prosthesis, training includes repetitive drills without objects, object manipulation, and finally, activities of daily living. Ultimately, regular patient appointments and functional assessments allow tracking prosthetic function and enabling early interventions if malfunctioning.