Objective To investigate the neuroprotective effect of Glycosides of cistanche (GCs) on cerebral ischemia reperfusion injury in rats and its mechanism. Methods Forty-eight male Wistar rats were randomly divided into Sham group, Model group, GCs group and Nim group. A rat model of focal cerebral ischemia reperfusion injury (CIRI) was established by middle cerebral artery occlusion (MCAO). Sticker removal test, balance beam test, and open field test were used to evaluate the sensory and motor abilities of rats in each group. TTC staining was used to detect the area of cerebral infarction, Nissl staining was used to observe the morphology of nerve cells, and TUNEL staining was used to detect the apoptosis of nerve cells. The expressions of apoptosis-related proteins Bax, Bcl-2 and 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), the time of removing stickers and passing balance beam was significantly increased (P < 0.01), the motor ability was decreased, the infarct size was increased, the number of neurons was decreased, and the number of apoptotic cells was increased after cerebral ischemia reperfusion. The expressions of Bax and Caspase-3 were significantly increased (P < 0.05), and the expression of Bcl-2/Bax was significantly decreased (P < 0.05). Compared with the Model group, GCs could improve the behavioral performance of cerebral ischemia reperfusion model rats, reduce the infarct size, inhibit cell apoptosis, down-regulate the expression of Bax and Caspase-3 (P < 0.05), and up-regulate the expression of Bcl-2/Bax (P < 0.05). Conclusion GCs has a neuroprotective effect on cerebral ischemia-reperfusion injury, which may play a role in inhibiting cell apoptosis by regulating the expression of apoptosis-related factors Bax, Bcl-2 and Caspase-3.