Background: Neuroinflammation plays an important role in neonatal hypoxic-ischemic encephalopathy (HIE). Although microglia are largely responsible for injury-induced inflammatory response, they play beneficial roles in both normal and disease states. However, the effects of microglial depletion on neonatal HIE remain unclear. Methods: Tamoxifen was administered to Cx3cr1 CreER/+ Rosa26 DTA/+ (microglia-depleted model) and Cx3cr1 CreER/+ Rosa26 DTA/− (control) mice at P8 and P9 to assess the effect of microglial depletion. The density of microglia was quantified using Iba-1 staining. Moreover, the proportion of resident microglia after the HI insult was analyzed using flow cytometric analysis. At P10, the HI insult was conducted using the Rice-Vannucci procedure at P10. The infarct size and apoptotic cells were analyzed at P13. Cytokine analyses were performed using quantitative polymerase chain reaction and enzyme-linked immunosorbent assay (ELISA) at P13.Results: At P10, tamoxifen administration induced > 99% microglial depletion in DTA + mice. Following HI insult, there was persisted microglial depletion over 97% at P13. Compared to male DTA − mice, male DTA + mice exhibited significantly larger infarct volumes; however, there were no significant differences among females. Moreover, compared to male DTA − mice, male DTA + mice had a significantly higher density of TUNEL + cells in the caudoputamen, cerebral cortex, and thalamus. Moreover, compared to female DTA − mice, female DTA + mice showed a significantly greater number of TUNEL + cells in the hippocampus and thalamus. Compared to DTA − mice, ELISA revealed significantly lower IL-10 and TGF-β levels in both male and female DTA + mice under both normal conditions and after HI (more pronounced). Conclusion: We established a microglial depletion model that aggravated neuronal damage and apoptosis after the HI insult, which was predominantly observed in males.