Objectives: The objective of this study was to assess bra in activation and difference by LI11 or ST36 acupuncture stimulation using functional MRI (fMRI). Methods: A total of 10 healthy right-handed volunteers were studied. LI11 acupuncture and ST36 acupuncture stimulations were applied in order on the left. The block design paradigm of RARARA was used for the task, with R representing rest and A representing stimulation, and each period lasted 30 seconds. fMRI data were analyzed using SPM2. Results: The left LI11 acupuncture stimulation activated both sides of the inferior parietal lobule, the left side of the extra-nuclear, culmen and inferior semi-lunar lobules. On the right side, the nodule and midbrain regions were activated by the left LI11 acupuncture stimulation. The left ST36 acupuncture stimulation activated the right side of the superior frontal gyrus, middle frontal gyrus, superior parietal lobule, inferior semi-lunar lobule and pyramis. On the left side, the sub-gyral, middle temporal gyrus, fusiform gyrus, supramarginal gyrus, extra-nuclear, cingulate gyrus and fastigium regions were activated by the left ST36 acupuncture stimulation. Besides, both sides of the paracentral lobule, inferior parietal lobule, culmen, cerebellar tonsil and midbrain regions were activated. Conclusions: In conclusion, brain signal activation patterns according to acupoints were observed to differ, and ST36 acupuncture stimulation activated more regions than LI11. It is supposed that LI11 and ST36 acupuncture stimulations have an influence on motor function and sensory aphasia, and these stimulations thus represent potential for ocular motor dysfunction, discriminative touch or position sense disorder. Moreover, ST36 acupuncture stimulation activated the cingulate gyrus of the limbic system, so it seems to have an influence over autonomic functions.