Fifty-eight patients with non-specific chronic low back pain (NCLBP) were randomized to receive motor control exercise (MCE) (n=30) or manual therapy (MT) (n=28). The primary outcome of interest was pain intensity, measured using the Visual Analog Scale (VAS). Secondary outcomes included pain-related disability (Oswestry Disability Index, ODI), pain characteristics (Short-Form McGill Pain Questionnaire, SFMPQ), and pain catastrophizing (Pain Catastrophizing Scale, PCS). Outcomes were assessed post-intervention and at a 6-month follow-up. Overall, the results revealed that MCE led to a significantly greater reduction in pain intensity and disability compared to MT, with sustained effects at the 6-month follow-up. Functional MRI analyses demonstrated that MCE induced changes in functional connectivity within the brain, particularly in the cerebellum and areas involved in pain processing, which were not observed in the MT group. These findings suggest that MCE not only alleviates pain but also modulates neural activity associated with chronic pain, supporting its use in rehabilitation strategies for NCLBP.