AbstractAdult neurogenesis continues throughout life but declines dramatically with age and in neurodegenerative disorders such as Alzheimer's disease. In parallel, microglia become activated resulting in chronic inflammation in the aged brain. A unique type of microglia, suggested to support neurogenesis, exists in the subventricular zone (SVZ), but little is known how they are affected by aging. We analyzed the transcriptome of aging microglia and identified a unique neuroprotective activation profile in aged SVZ microglia, which is partly shared with disease‐associated microglia (DAM). CX3C motif chemokine receptor 1 (CX3CR1) is characteristically expressed by brain microglia where it directs migration to targets for phagocytosis. We show that Cx3cr1 expression, as in DAM, is downregulated in old SVZ microglia and that heterozygous Cx3cr1 mice have increased proliferation and neuroblast number in the aged SVZ but not in the dentate gyrus, identifying CX3CR1 signaling as a novel age and brain region‐specific regulator of neurogenesis.