Cerebral ischemia is a serious neurological disorder that can lead to high morbidity and mortality. Baicalin is a naturally bioactive flavonoid derived from Scutellaria baicalensis Georgi, which has neuroprotective activity. Baicalin exerts a neuroprotective effect against hypoxic ischemic injury. In this study, we investigated whether baicalin regulates specific proteins in the cerebral cortex of ischemic stroke animals. Middle cerebral artery occlusion (MCAO) surgery was performed to induce ischemic brain injury, and baicalin (30 mg/kg) or vehicle was injected into the abdominal cavity before MCAO surgery. Neurological behavior tests were performed 24 h after MCAO surgery and proteomics approach was performed using proteins extracted from cortical tissue. Two-dimensional electrophoresis analysis and MALDI-TOF were performed to identify the regulated protein by baicalin. MCAO damage caused severe behavioral disorders, but baicalin treatment improved these behavioral deficits. Baicalin also induced changes in the expression of various proteins in the cerebral cortex of MCAO animals. Proteins changed by baicalin administration are as follow: adenosylhomocysteinase, isocitrate dehydrogenase [NAD] subunit alpha, apolipoprotein A-I, Rab GDP dissociation inhibitor beta, eukaryotic initiation factor 4A, and mu-crystallin. These proteins were involved in metabolism and protein synthesis. The results of this study demonstrated the neuroprotective effects of baicalin by improving behavioral disorders caused by MCAO damage. The results also showed that baicalin regulates the expression of a variety of proteins involved in neuroprotective functions. Therefore, our findings provide evidence that baicalin plays a neuroprotective role in stroke animal models by regulating specific proteins.