Acupuncture is an alternative treatment for primary dysmenorrhea (PDM). However, mechanisms by which acupuncture exerts its analgesic properties are still unclear. This study aimed to explore the cerebral blood flow (CBF) response to verum and sham acupuncture treatments, and further investigate whether pre-treatment CBF is capable of assessing symptom changes after interventions. A total of 11 PDM patients in the verum group and 12 patients in the sham group participated in this study. Pain rating index (PRI), CBF, and gonadal hormone levels were acquired before and after 8-week treatments. Both verum and sham acupuncture treatments exert its analgesic effect on PDM after intervention as PRI reduced (p < 0.05). Blood gonadal levels were not significantly different after acupuncture in both groups (all p > 0.05). In the verum group, intervention-related decreases in CBF were observed in the right dorsal anterior cingulate cortex. In the sham group, regions identified as showing reductions in CBF after acupuncture included the left ventromedial prefrontal cortex, left caudate, and left insula. Patients with higher baseline CBF in the left precuneus and right hippocampus were accompanied with worse treatment response to acupuncture intervention. Mechanisms of verum and sham acupuncture treatments are dissimilar as manifested by different brain responses.