Conventional neuroimaging techniques cannot truly reflect the change of regional cerebral blood flow in patients with carpal tunnel syndrome. Pseudo-continuous arterial spinning labeling (pCASL) as an efficient non-invasive neuroimaging technique can be applied to directly quantify the neuronal activities of individual brain regions that show the persistent symptoms owing to its better spatial resolution and increased signal-to-noise ratio. Therefore, this prospective observational study was conducted in 27 eligible female carpal tunnel syndrome, aged 57.7 ± 6.51 years. Psychometric tests, nerve conduction studies and pCASL neuroimaging assessment were performed. The results showed that the relevant activated brain regions in the cortical, subcrotical, and cerebral regions were correlated with numbness, pain, functionality, median nerve status and motor amplitude of median nerve (K = 21-2849, r = -0.77-0.76, P < 0.05). There was a tendency of pain processing which shifted from the nociceptive circuitry to the emotional and cognitive one during the process of chronic pain caused by carpal tunnel syndrome. It suggests the necessity of addressing the ignored cognitive or emotional state when managing patients with carpal tunnel syndrome. Approval for this study was obtained from the Institutional Review Board of The University of Hong Kong/Hospital Authority Hong Kong West, China (HKU/HA HKW IRB, approval No. UW17-129) on April 11, 2017. This study was registered in Clinical Trial Registry of The University of Hong Kong, China (registration number: HKUCTR-2220) on April 24, 2017.