Microglia are macrophage-like phagocytic cells in the brain parenchyma. However, microglial function after neurodegeneration is not fully understood. In this study, occlusion of the middle cerebral artery (MCA) and reperfusion caused massive neuronal loss in the rat cerebral cortex and striatum after 3 days. When exogenous microglia were microinjected into the intracerebroventricle during MCA occlusion, neurodegenerative areas significantly decreased. At that time, migrated microglia were detected in the ischemic lesion. These results suggest that exogenous microglia can migrate into brain parenchyma and then protect against neurodegeneration induced by MCA occlusion and reperfusion.