Ischemic stroke leads to liquefactive necrosis, which disappears from intracranial space with the passage of time. The necrotic tissue contains various types of neurotoxic components. Thus, effective clearance of necrotic debris is important for non-necrotic areas to maintain homeostasis. However, the precise mechanism of necrotic tissue drainage is not revealed. Currently, we found that endothelial cells proliferation was significantly upregulated in the necrotic area at 3 days after middle cerebral artery occlusion (MCAO). Concomitantly, microglia were induced in the necrotic area. Microglial depletion by PLX3397 administration significantly inhibited the MCAO-induced endothelial cells proliferation. Furthermore, disappearance of necrotic tissue was significantly inhibited by microglial depletion. These results suggest that the necrotic tissue is drained through the vessels in the necrotic tissue, which is provided by microglia.