Microglial cells of the aged brain manifest signs of dysfunction that could contribute to the worse neurological outcome of stroke in the elderly. Treatment with colony-stimulating factor-1 receptor antagonists enable transient microglia depletion that can be followed by microglia repopulation after interruption of the treatment, causing no known harm to mice. Using this strategy, we aimed to restore microglia function and ameliorate stroke outcome in aged mice. Cerebral ischemia/reperfusion induces strong innate immune responses in microglia highlighted by prominent type I interferon signaling, together with cellular metabolic perturbances and lipid droplet biogenesis in young mice. In aged mice, a subset of microglia accumulates lipid droplets under steady state and displays exacerbated innate immune responses after stroke. Microglia renewal in old mice reduces the lipid droplet content, prevents the ischemia-induced exaggerated type I interferon response, and improves the neurological outcome of stroke. This study shows that age-dependent lipid droplet-enriched microglia contribute to impair stroke outcome in old mice.