Ischemic stroke is a fatal disease that has long-term disability. It induces excessive oxidative stress generation and cellular metabolic disorders, result in tissue damage. Epigallocatechin gallate (EGCG) is a naturally derived flavonoid with strong antioxidant property. We previously reported the neuroprotective effect of EGCG in ischemic stroke. The defensive mechanisms of stroke are very diverse and complex. This study investigated specific proteins that are regulated by EGCG treatment in the ischemic brain damage. Middle cerebral artery occlusion (MCAO) was performed to induce focal cerebral ischemia. EGCG (50 mg/kg) or vehicle was intraperitoneally administered just prior to MCAO. MCAO induced severe neurological deficits and disorders. EGCG treatment alleviated these neurological disorder and damage. Cerebral cortex was used for this study. Two-dimensional gel electrophoresis and mass spectrometry were performed to detect the proteins altered by EGCG. We identified various proteins that were changed between vehicle- and EGCG-treated animals. Among these proteins, isocitrate dehydrogenase, dynamin-like protein 1, and γ-enolase were decreased in vehicle-treated animals, while EGCG treatment prevented these decreases. However, pyridoxal-5'-phosphate phosphatase and 60 kDa heat shock protein were increased in vehicle-treated animals with MCAO injury. EGCG treatment attenuated these increases. The changes in these proteins were confirmed by Western blot and reverse transcription-PCR analyses. These proteins were associated with cellular metabolism and neuronal regeneration. Thus, these findings can suggest that EGCG performs a defensive mechanism in ischemic damage by regulating specific proteins related to energy metabolism and neuronal protection.