Chronic cerebral hypoperfusion (CCH) is manifested in a various CNS diseases, including neurodegenerative and mental disorders accompanied by cognitive impairment. We previously demonstrated that microglial activation via TRPM2, a Ca²⁺-permeable non-selective cation channel, induced excessive inflammatory responses, white matter injury, and resultant aggravation of cognitive impairment in a mouse CCH model with bilateral common carotid artery stenosis (BCAS), while there was no direct evidence on the contribution of microglia. To clarify the role of microglia in the BCAS model, we used PLX3397, an orally-active inhibitor of colony-stimulating factor 1 receptor (CSF1R), since microglia require CSF1R signaling for survival. When mice were fed with PLX3397-containing chow at 290 mg/kg for 3 weeks, virtually all Iba1-immunopositive microglia were eliminated from the brains, without obvious deficits in the behaviors. When the mice were then subjected to BCAS, white matter injury and cognitive dysfunction at additional 28 days were improved in the PLX3397-fed mice compared with control mice. These results suggest that microglia play destructive roles in the development of CCH-induced cognitive impairment.