Neonatal encephalopathy is a neurological emergency with heterogeneous etiologies and several management challenges. Neonatal encephalopathy of hypoxic-ischemic origin is associated with high rate of neonatal morbidity and mortality, and the long-term neurodevelopmental outcome of survivors with moderate to severe encephalopathy is poor. Magnetic resonance imaging now provides new insights on the diagnosis and prognosis of this condition. Typical patterns of brain injury have been recognized and in contemporary cohorts of newborns these patterns reflect different risk factors and clinical presentation, as well as specific patterns of neurodevelopmental outcome. Magnetic resonance spectroscopy, diffusion-weighted imaging, and diffusion tensor imaging are advanced MR techniques that are increasingly used in the assessment of encephalopathic newborns, providing innovative perspectives on neonatal brain metabolism, microstructure, and connectivity. These techniques have been particularly helpful in elucidating the unique time course of neonatal brain injury and in providing quantitative biomarkers for prognostication. To better refine the prognostic value of these new imaging tools, standardization of protocols, imaging modalities and scan timing are needed across centers. It is hoped that these techniques will permit earlier identification of newborns at risk of neurodevelopmental impairment and complement ongoing trials of emerging therapies such as hypothermia and novel pharmacological agents with neuroprotective properties.