The Notch1 signaling pathway plays a crucial role in the development of the central nervous system, governing pivotal functional activities in the brain, such as neurogenesis. Sirt3 is instrumental in managing mitochondrial homeostasis and is essential to cell survival. Dysregulation of these signaling pathways is implicated in the pathogenesis of a wide range of diseases, including neurodegenerative disorders such as stroke. We have previously shown that melatonin significantly improved the perinatal brain damage caused by hypoxia-ischemia (HI) through the activation of several protective mechanisms such as restoring mitochondria status and increasing the hippocampal cell proliferation. This study assessed whether melatonin affects the Notch1 signaling pathway and Sirt3 after neonatal HI. Results show that HI significantly increased Notch1 expression both in hippocampal neurons and glial cells as well as the expression of the key proteins of the pathway NICD, HES1, and c-Myc. Melatonin significantly prevented the Notch1 signaling pathway activation induced by HI, maintaining NICD and HES1 expression to control levels. In the same neurons, melatonin also prevents the Sirt3 depletion caused by HI. In summary, this study provides new insights into the effects of melatonin on the Notch1 signaling pathway and Sirt3 in in vivo neonatal brain ischemia. We suggest that the rapid modulation of the Notch1 signaling pathway and Sirt3 induced by melatonin may support neuronal survival during ischemia.