Objective: To investigate the effects of spinal manipulation (SM) on brain functional activity in patients with lumbar disc herniation (LDH). Methods: Eleven patients with LDH were recruited in the study. All patients received 6 times of lumbar SM treatment and then clinical efficacy was evaluated. All patients received brain functional magnetic resonance imaging (fMRI) scans before and after SM treatment. Results: Three subjects dropped out and 8 subjects completed the study, among whom 4 cases were effective and 4 ineffective after SM treatment. The required pressure value producing the same level (VAS 50) pain was (7.43 ± 1.47) kg and (10.53 ± 0.55) kg before and after SM treatment in effective patients(P<0.05); however, there was no significant difference in ineffective patients (P>0.05). Compared to pre-treatment level, the brain functional activity in effective patients was mainly inhibited, the inhibited areas were located in the right side of prefrontal cortex and cerebellum; while the brain functional activity was generally enhanced in ineffective patients. Conclusion: SM can affect the brain functional activity of patients with LDH, the inhibited areas is mainly located in prefrontal cortex and cerebellum when SM treatment is effective.