Objective This study investigated the impact of neurofeedback training on the deeper cortical structures that comprise the “pain matrix” and are involved in processing neuropsychological functions.Methods Five paraplegic patients with central neuropathic pain received up to 40 sessions of neurofeedback training. They were asked to simultaneously modulate the relative power of the theta, alpha and beta bands, provided as a feedback from the sensorimotor cortex. The source localization technique was applied on EEG data recorded with 16 electrodes placed over the whole head.ResultsNeurofeedback training from the sensorimotor cortex induced effects on the pain matrix and in the areas involved in processing neuropsychological functions such as memory, executive functions and emotional regulations. Alpha and beta band activity was most increased in insular, cingulate and frontal cortex regions, and other areas corresponding to executive and emotional function processing. Theta band decreases were noted in the frontal, cingulate and motor cortices. In group analysis, theta and beta band activity was significantly reduced.Conclusion The single channel electroencephalogram-based neurofeedback training produced effects on similar areas that are targeted in 19 channels standardized low-resolution brain electromagnetic tomography and expensive time-delayed functional magnetic resonance imaging feedback studies.