In neonatal intensive care units, there is a need for continuous monitoring of sick newborns with perinatal hypoxic ischemic brain injury (HIE). We assessed the utility of heart rate variability (HRV) in newborns with acute HIE undergoing simultaneous continuous EEG (cEEG) and ECG monitoring. HIE was classified using clinical criteria as well as visual grading of cEEG. Newborns were divided into two groups depending on the severity of the hypoxic injury and outcome. Various HRV parameters were compared between these groups, and significantly decreased HRV was found in neonates with severe HIE. As HRV is affected by many factors, it is difficult to attribute this difference solely to HIE. However, this study suggests that further investigation of HRV as a monitoring tool for acute neonatal hypoxic injury is warranted.