Neonatal hypoxic-ischemic encephalopathy is aggravated by intracerebral inflammation. As pro-inflammatory microglia in the brain become activated in this condition, we aimed to establish a novel peptide therapy for neonatal hypoxic-ischemic encephalopathy by investigating the therapeutic effects of pro-inflammatory microglial depletion. MG1 homing peptide, which selectively targets and binds pro-inflammatory microglia, was conjugated with the pro-apoptotic peptide D[KLAKLAK]2 (KLA), creating MG1-KLA. After confirming that MG1-KLA selectively bound pro-inflammatory microglia and decreased cell viability by inducing apoptosis in a dose-dependent manner, the in vivo therapeutic effect of MG1-KLA was assessed following intracerebroventricular injection in hypoxic-ischemic encephalopathy model mice through histological, behavioral, and biochemical analyses. In these mice, MG1-KLA selectively bound to microglia and induced their apoptosis. Brain atrophy was significantly suppressed in the mice treated with MG1-KLA compared with non-treated mice. Additionally, motor function and locomotor hyperactivity were improved in mice treated with MG1-KLA compared with non-treated mice. Gene expression analysis further revealed that pro-inflammatory cytokine expression was downregulated in mice treated with MG1-KLA compared with non-treated mice. These findings suggest that the novel MG1-KLA peptide therapy has high potential for treating neonatal patients with hypoxic-ischemic encephalopathy through the selective induction of apoptosis in pro-inflammatory microglia.