Objective To investigate the influence of bone marrow mesenchymal stem cell (BMSCs) transplantation on the protein expression of miR-34a and survivin in the brain tissue in rats with ischemia-reperfusion injury, as well as the anti-apoptotic and neuroprotective effects of BMSCs transplantation.Methods A total of 192 rats were randomly divided into blank group, model group, PBS transplantation group, and stem cell transplantation group. The modified Longa suture method was used to establish the rat model of middle cerebral artery occlusion (MCAO), and tail vein injection was performed for stem cell transplantation. The modified neurological severity score (mNSS) was used to evaluate neurological defects, immunohistochemistry was used to measure the protein expression of survivin, and quantitative real-time PCR was used to measure the protein expression of miR-34a.Results The mNSS scores at 12 hours and day 1 showed no significant differences between the stem cell transplantation group and the model group (P>0.05), while compared with the model group, the stem cell transplantation group had significantly lower mNSS scores on days 3 and 7 (P<0.05). Compared with the model group, the stem cell transplantation group had significantly higher rates of survivin-positive cells at all time points (P<0.05), and significantly lower protein expression of miR-34a at all time points (P<0.01).Conclusions The ischemia-reperfusion injury in brain upregulates the protein expression of miR-34a in lesions, and stem cell transplantation can significantly improve the neurological function in rats with ischemia-reperfusion. Stem cell transplantation exerts its anti-apoptotic and neuroprotective effects through downregulating miR-34a and upregulating survivin in lesions.