Many factors acting during the neonatal period can affect neurological development of the infant. Neonatal seizures (NS) that frequently occur in the immature brain may influence autonomic maturation and lead to detectable cardiovascular signs. These autonomic manifestations can also have significant diagnostic and prognostic value. The analysis of Heart Rate Variability (HRV) represents the most used and feasible method to evaluate cardiac autonomic regulation. This narrative review summarizes studies investigating HRV dynamics in newborns with seizures, with the aim of highlighting the potential utility of HRV measures for seizure detection and management. While HRV analysis in critically ill newborns is influenced by many potential confounders, we suggest that it can enhance the ability to better diagnose seizures in the clinical setting. We present potential applications of the analysis of HRV, which could have a useful future role, beyond the research setting.