The brain motor control assessment (BMCA) for the upper limb has been developed to add resolution to the clinical evaluation in patients with spinal cord injury (SCI). BMCA is a surface electromyography (sEMG)-based measure of motor output from the central nervous system during a variety of reflex and voluntary motor tasks performed under strictly controlled conditions.Nine participants were recruited and assessed four times over a period of 1 year in a prospective cohort study design. The sEMG of 15 muscles (7 muscles from each upper limb and rectus abdominis) were recorded throughout the following stages of the BMCA protocol: (i) relaxation, (ii) reinforcement maneuvers, (iii) voluntary tasks, (iv) tendon-tap reflex responses, (v) vibration responses.Similarity index (SI) values were significantly lower in the SCI group for unilateral shoulder abduction (P = 0.006) and adduction (P = 0.021), elbow extension (P = 0.038), wrist flexion/extension with palm up (P < 0.001; P < 0.001) and wrist flexion with palm down (P = 0.016). sEMG magnitudes were also significantly lower in the SCI group for wrist flexion/extension with palm up (P < 0.001; P = 0.042). SI changes over time were significant for tasks related to wrist joint (P = 0.002).Clinicians who are involved in rehabilitation of patients with SCI can use the BMCA to assess their patients' motor control abilities and monitor their progression throughout their rehabilitation process. The results of this type of neurophysiological assessment might be useful to tailor therapeutic strategies for each patient.