Objective To investigate the neuroprotective effect and mechanism of glycosides of Cistanche (GCs) on cerebral ischemia reperfusion injury (CIRI) in rats. Methods Forty-eight male Wistar rats were divided randomly into Sham, Model, GCs, and Nim groups. A rat model of focal CIRI was established by middle cerebral artery occlusion. Neurological function was scored using the Zea-Longa scoring method. The sensory and motor abilities of rats in each group were evaluated by sticker removal, balance beam, and open field tests. The area of cerebral infarction was detected by 2,3,5-triphenyltetrazolium chloride(TTC) staining, Nissl staining was used to observe the morphology of nerve cells, and terminal deoxynucleotidyl transferase dUTP nick end labeling was used to detect apoptosis of nerve cells. Expression levels of the apoptosis-related proteins B-cell lymphoma-2 (Bcl-2), Bcl-2 associated X (Bax), and cysteine aspartic protease-3 (Caspase-3) were detected by immunohistochemical staining and Western blot. Results Compared with the Sham group, the neurological deficit score was significantly increased (P<0.05) and the times to remove stickers and passing the balance beam were significantly increased (P<0.05), motor ability was decreased, infarct size was increased, the number of neurons was decreased, and the number of apoptotic cells was increased after CIRI. Bax and Caspase-3 expression were significantly increased (P<0.05) and Bcl-2/Bax was significantly decreased (P<0.05). Compared with the Model group, GCs improved the behavioral performance of CIRI model rats, reduced the infarct size, inhibited cell apoptosis, downregulated the expression of Bax and Caspase-3 (P<0.05), and up-regulated the expression of Bcl-2/Bax (P<0.05). Conclusions GCs have a neuroprotective effect on CIRI, and may play a role in inhibiting cell apoptosis by regulating the expression of the apoptosis-related factors Bax, Bcl-2, and Caspase-3.