Transient brain hypoxia-ischemia (HI) in neonates leads to delayed neuronal death and long-term neurological deficits. However, the underlying mechanisms are incompletely understood. Calcium-calmodulin-dependent protein kinase II (CaMKII) is one of the most abundant protein kinases in neurons and plays crucial roles in synaptic development and plasticity. This study used a neonatal brain HI model to investigate whether and how CaMKII was altered after HI and how the changes were affected by brain development. Expression of CaMKII was markedly up-regulated during brain development. After HI, CaMKII was totally and permanently depleted from the cytosol and concomitantly deposited into a Triton-insoluble fraction in neurons that were undergoing delayed neuronal death. Autophosphorylation of CaMKII-Thr286 transiently increased at 30 min of reperfusion and declined thereafter. All these changes were mild in P7 pups but more dramatic in P26 rats, consistent with the development-dependent CaMKII expression in neurons. The results suggest that long-term CaMKII depletion from the cytosolic fraction and deposition into the Triton-insoluble fraction may disable synaptic development, damage synaptic plasticity, and contribute to delayed neuronal death and long-term synaptic deficits after transient HI.