Chronic neuropathic pain may require a neurosurgical treatment, but for reasons that have not been fully explored yet, a significant number of patients do not benefit from the intervention. We compared the resting EEG of 15 healthy controls to the EEG of 23 chronic neuropathic pain patients before and 12 months after treatment by the central lateral thalamotomy (CLT). A patient subgroup had a high (n = 14, pain relief (PR) ≥ 50%) and another subgroup a low (n = 9, PR < 50%) postoperative PR. EEG spectral power and source localization of the high PR patients were normalized postoperatively. In contrast, low PR patients showed postoperative maintenance of insular, cingulate and prefrontal overactivities, and their frustration values were positively correlated with cingulate and prefrontal activity. These findings demonstrate a normalizing effect of CLT on cortical activity and suggest that treatment resistance is associated with a frustration-based dynamics.