Balanced acupuncture, a single-acupoint balance therapy, regulates the balance of the cerebral center, and is characterized by exerting quick effects and a short treatment course. A total of 20 low-back and leg pain patients with lumbar disc hemiation were treated with balanced acupuncture or body acupuncture. Central mechanisms of varied acupunctures were compared using resting-state functional MRI. Patients from both groups received functional MRI before and after acupuncture. Functional connectivity in brain regions that were strongly associated with the bilateral amygdala was analyzed utilizing AFNI software. Visual analogue scale scores were greater in the balanced acupuncture group compared with the body acupuncture group. Function of the endogenous pain regulation network was enhanced in patients in the balanced acupuncture group, but was not changed in the body acupuncture group. This result indicates that the analgesic effects of body acupuncture do not work through the central nervous system. These data suggest that balanced acupuncture exerts analgesic effects on low-back and leg pain patients with lumbar disc herniation by regulating the function of the endogenous pain regulation network.