To implore the effect and mechanism of exercise preconditioning on neurological deficits in rats with cerebral ischemia-reperfusion (MCAO/R).Thirty-six healthy Sprague-Dawley rats were divided into model group, sham operation group and exercise preconditioning group according to the random number table. Each group consisted of 12 rats (n=12). A rat model of cerebral ischemia-reperfusion (MCAO/R) was established by modified suture method. After 2h, 12h, 24h of reperfusion, neurological impairment was evaluated by neurological deficit score. After 24h reperfusion, the expressions of mitoKATP channel protein Kir6.2 and SUR1 were detected by Western blot, the cerebral cell apoptosis was detected by TUENL assay.Compared with model group, neurological deficit scores of rats in exercise preconditioning group were significantly decreased (P<0.05). Compared with model group, exercise preconditioning group Kir6.2, SUR1 protein level and TUNEL-positive cells decreased significantly (P<0.05).Exercise preconditioning may improve neurological impairment after cerebral ischemia by regulating the expression of mitoKATP channel proteins Kir6.2, SUR1 and cell apoptosis.