Aim To observe the effect of electroacupuncture (EA) at Quchi and Zusanli acupoint on the expressions of cortical synaptophysin (SYN) and brain-derived neurotrophic factor (BDNF) in cerebral ischemia model rats, and to explore the mechanism of EA in the treatment of ischemic stroke. Methods 90 rats were randomly divided into sham operation group, model group and EA group, and each group was divided into 3 subgroups according to time points:3 days group, 7 days group, 14 days group, 10 rats in each subgroup. Left middle cerebral artery occlusion model was established by modified suture plug method in model group and EA group. Neurological deficit score was scored at 2 h after operation and before death. EA group received EA at affected side Quchi and Zusanli acupoint, 1 time each day, 30 minutes each time, until the animal was killed. Immunohistochemical staining, Western blot and reverse transcription polymerase chain reaction (RT-PCR) were used to detect the expression of SYN and BDNF in the left cortex of rats. Results Compared with sham operation group, the neurological deficit scores of model group and EA group were significantly increased (P＜0.01); after EA treatment, the neurological deficit score of EA group was lower than that of model group (P＜0.05). Immunohistochemical staining and Western blot results showed that compared with sham operation group, the expression of SYN protein was significantly decreased in model group and EA group, and the expression of SYN protein in EA group was significantly higher than that in model group (P＜0.01); Compared with sham operation group, the expression of BDNF protein was significantly increased in model group and EA group, and the expression of BDNF protein in EA group was significantly higher than that in model group (P＜0.01). RT-PCR results showed that compared with sham operation group, the expression of SYN mRNA was significantly decreased in model group and EA group, and the expression of SYN mRNA in EA group was significantly higher than that in model group (P＜0.01); Compared with sham operation group, the expression of BDNF mRNA was significantly increased in model group and EA group, and the expression of BDNF mRNA in EA group was significantly higher than that in model group (P＜0.01). Conclusion Electroacupuncture at Quchi and Zusanli acupoint can promote the synthesis and secretion of BDNF in the cerebral cortex of rats with cerebral ischemia, and increase the expression of SYN, which may play an important role in the regulation of brain plasticity.