Background: Heart Rate Variability (HRV) originates from the interplay between parasympathetic/sympathetic inputs to the heart, thus serving as an indicator of Autonomic Nervous System regulation. Prior research indicates that decreased HRV, marked by reduced autonomic balance, is related to poorer cognitive performance. While the population with congenital heart disease (CHD) show changes in HRV linked with the heart defect, the association between HRV and cognitive functions in CHD remains unexplored., Methods: 46 adolescents with CHD who went through infant open-heart surgery and 64 healthy controls (50.9% males, 12.8 ± 1.4 years) underwent neurodevelopmental testing and photoplethysmograph acquisition. Group differences and associations with cognitive functions were analysed with linear regression. P values were FDR-corrected., Results: Adolescents with CHD showed lower HRV (quantified by high-frequency power) compared to controls (p < 0.001). Lower HRV was correlated with worse executive function (β = 0.24, p = 0.044) and lower IQ (β = 0.26, p = 0.010) in the whole sample and with lower IQ (β = 0.35, p = 0.014) in the CHD group. These associations were robust to confounders, including age, sex, and socioeconomic status., Conclusion: Our findings demonstrate an association between HRV and cognitive functions in adolescents with complex CHD. Early detection of alterations in HRV/autonomic regulation may help to identify children with CHD at risk for cognitive impairments., Impact: Adolescents with congenital heart disease (CHD) showed lower heart rate variability (HRV), indicating an imbalanced autonomic nervous system. Lower HRV was associated with lower IQ and executive function (EF) in the whole sample. The association between HRV and IQ was significantly stronger in CHD than in healthy controls. This study provides the first evidence of a link between altered HRV and cognitive impairments in the CHD population. Neurodevelopmental impairments seen in adolescents with CHD could be linked to their altered cardiac autonomic nervous activity, marked by low HRV., (© 2024. The Author(s).)