This systematic review with a meta-analysis aimed to identify the altered brain structure and function in carpal tunnel syndrome (CTS) by summarizing the literature about magnetic resonance imaging (MRI), functional magnetic resonance imaging (fMRI), and magnetoencephalography (MEG) outcomes compared to healthy controls (HC). CTS is the most common nerve entrapment in the arm associated with altered peripheral and central nociceptive system. PRISMA guidelines were used to report the outcomes. Six databases were searched for relevant literature (Web of Science, Scopus, PubMed, Sage, EBSCO host, and Cochrane). Eligible studies comparing MRI, fMRI, and MEG findings in people with CTS (present for at least 2months) and HC through the following parameters: (1) interdigit cortical separation distance, (2) white and grey matter changes, (3) peak latency of M20 wave and recovery function of N20 from the somatosensory cortex (SI), and (4) surface area of activated digit cortical representation. The results from different studies were pooled and a meta-analysis was done. From 17 included, there was a significant reduction of interdigit cortical separation distance of index-middle and index-little fingers in the CTS (SMD = -0.869, 95% CI (-1.325, -0.413), p-value = 0.000) and (SMD = -0.79, 95% CI (-1.217, -0.364), p-value = 0.000), respectively. Middle-little fingers interdigit separation showed no difference (SMD = -0.2, 95% CI (-0.903, 1.309), p-value = 0.718). There is evidence supporting the altered brain structure and function in CTS as evidenced by reduction of interdigit cortical separation distance, and excessive blurring and disinhibition of SI, with low resting state functional connectivity. Thus, centrally directed therapeutic approaches might complement peripheral treatments.