Hypoxic ischemic encephalopathy (HIE) is a severe neonatal condition causing various neurological disorders and one of the main causes of mortality among full-term babies. Therapeutic hypothermia (TH), i.e. the newborn’s body temperature decrease that significantly reduces the risk of fatality and contributes to improvement of long-term outcomes in infants with HIE is the key treatment method for moderate-to-severe HIE. However, the timely diagnosis and disease severity determination are crucial for this method to be used, and the method has a number of limitations and requirements. Assessment of the mechanism underlying the effects of TH and the search for the major metabolic pathways and potential targets for HIE therapy are relevant. The study aimed to assess metabolome of dried blood spots by HPLC-MS, since it is the least invasive to patients test for the search for markers and metabolic pathways most active in TH that are likely to mediate its positive effects. As a result, alterations in the class of phosphoglycerolipids were found, which suggests an important role of endocannabinoid metabolism in protection of the body against HIE. Furthermore, metabolic pathways of ubiquinone, certain fatty acids, and bile acids were altered. The targeted quantitative studies of these metabolites will make it possible to optimize HIE diagnosis and treatment based on the potential targets identified.