This study aimed to observe the effects of 3'-daidzein sulfonate sodium (DSS) on ischemia-reperfusion-induced brain injury and to analyze the mechanisms responsible for neuronal apoptosis. Focal ischemias were induced in male Sprague-Dawley rats using middle cerebral artery occlusion. The rats were divided into 5 groups based on sham surgery or real occlusion, and treatment with different doses of DSS (0.5, 1.0 and 2.0 mg/kg) or normal saline (model group), injected preoperatively into the rats with cerebral occlusion. After 2 h of ischemia and 24 h of reperfusion, neurological deficit scores were evaluated using the Longa grade point standard. The infarct volume was measured using a triphenyl tetrazolium chloride staining technique. Blood-brain barrier (BBB) permeability was measured using the Evans blue (EB) content of brain tissues, while electron microscopy was used to observe ultrastructural changes. The expression levels of Bcl-2, Bax and caspase-3 were detected by an immunohistochemical method and western blot analysis. The neurological deficit in rats pre-treated with DSS at all doses decreased significantly (P<0.05) in comparison with the model group, as did the cerebral infarct volume ratios. The brain EB content was significantly reduced by the injection of DSS. The ultrastructural integrity of the rat BBB was significantly preserved in the DSS-treated groups in comparison with the model group. This was concomitant with the reduced swelling of astrocytes and pericytes in the BBB. The immunohistochemistry results revealed that DSS significantly enhanced the expression of Bcl-2, and inhibited the expression of Bax and caspase-3 in the brain in comparison to the model group. The number of apoptotic cells in the groups treated with DSS was reduced in comparison with similar areas in the model group. These findings suggest that DSS within a dosage range of 0.5-2.0 mg/kg provides significant protection from injury to the BBB induced by cerebral ischemia-reperfusion, as it exerts a neuroprotective effect by inhibiting apoptosis.