In recent years, the increase of psychopathological disorders in the population has become a health emergency, leading to a great effort to understand psychological vulnerability mechanisms. In this scenario, the role of the autonomic nervous system (ANS) has become increasingly important. This study investigated the association between ANS, social skills, and psychopathological functioning in children. As an ANS status proxy, we measured heart rate variability (HRV). Infants admitted to the neonatal intensive care unit of the University Hospital of Padova because of preterm birth or neonatal hypoxic-ischemic encephalopathy were sequentially recruited from January 2011 to June 2013 and followed long-term up to school age in this cross-sectional observational study. We recorded 5 minutes of HRV immediately before measuring performance in social abilities tasks (affect recognition and theory of mind, NEPSY-II) in 50 children (mean age 7.4 ± 1.4 years) with and without risk factors for developing neuropsychiatric disorders due to pre-/perinatal insults without major sequelae. Children also completed extensive cognitive, neuropsychological, and psychosocial assessment. Parents were assessed with psychopathological interviews and a questionnaire (CBCL 6-18). Analysis in a robust Bayesian framework was used to unearth dependencies between HRV, social skills, and psychopathological functioning. Social task scores were associated with HRV components, with high frequency the most consistent. HRV bands were also associated with the psychopathological questionnaire. Only normalized HRV high frequency was able to distinguish impaired children in the affect recognition task. Our data suggest that ANS may be implicated in social cognition both in typical and atypical developmental conditions and that HRV has cross-disease sensitivity. We suggest that HRV parameters may reflect a neurobiological vulnerability to psychopathology. The study was approved by the Ethics Committee of the University Hospital of Padova (Comitato Etico per la Sperimentazione, Azienda Opedaliera di Padova, approval No. 1693P).