Brachial plexus injury may induce complete loss of sensation and motor control in parts of the affected arm, leading to phantom limb pain (PLP). PLP is associated with functional reorganization at the somatosensory cortex and alteration in the functional connectivity of the related pain brain areas. Several therapies have previously been suggested for PLP relief. Transcutaneous electrical nerve stimulation (TENS) is a non-invasive intervention used for pain relief and stroke rehabilitation. However, the underlying mechanism of TENS on cortical activity associated with PLP relief is not well-known. The effect of TENS (20Hz) intervention on somatosensory activity, cortical functional connectivity, and possible PLP reduction was investigated in this study in the case of a 55 year old subject with brachial plexus injury inducing complete paralysis below the elbow in the left arm. We recorded EEG data and the patient's pain level before and after the intervention. Somatosensory evoked potentials (SEPs) and functional connectivity between pain-related areas were assessed from EEG data. The results showed that the application of TENS suppressed somatosensory evoked potentials. In addition, the intervention enhanced the functional connectivity (a) between the primary somatosensory cortex and the anterior cingulate cortex (SI-ACC), also (b) between the primary somatosensory cortex and the medial prefrontal cortex (SI-MPC). Moreover, these results were associated with PLP reduction following TENS. We compared the results with our previous research on a large healthy population to assess the cortical changes.