Objective To investigate the effect of electroacupuncture (EA) at Quchi (LI11) and Zusanli (ST36) acupoints on rats with focal cerebral ischemia, and whether it was mediated by microRNA- 9 (miR- 9) regulating neural stem cells proliferation in subventricular zone. Methods Fifty-two Sprague-Dawley rats were randomly assigned into sham group (n=12), model group (n=12), EA group (n=12), EA+dimethylsulfoxide (DMSO) group (n=8) and EA+miR-9 mimics group (n=8). The middle cerebral artery occlusion model was induced. DMSO and miR-9 mimics were performed by intracerebroventricular injection 30 minutes before modeling. The EA group, EA+ DMSO group and EA+miR-9 mimics group were electroacupunctured at Quchi and Zusanli acupoints the next day after modeling. All the groups were intraperitoneally injected with bromodeoxyuridine (BrdU). The BrdU co-localized with Nestin was observed by immunofluorescence. The expression of miR-9 in subventricular zone was detected by real time qPCR. Results The neurological deficit score was lower (t=9.600, P=0.006), and the infarct volume was smaller (t=14.080, P=0.024) in the electroacupuncture group than in the model group. The expression of Nestin and BrdU co-localizated with Nestin increased; while the expression of miR-9 decreased in subventricular zone (P<0.05) in the electoacupuncture group. However, the expression of Nestin, BrdU and BrdU co-localizated with Nestin was lower in the EA+miR-9 mimics group than in the EA+ DMSO group. Conclusion Electroacupuncture at Quchi and Zusanli acupoints may promote the neural stem cells proliferation in subventricular zone by downregulating the miR-9 expression.