Objective Central systolic blood pressure (SBP) is a measure of arterial stiffness and strongly associated with atherosclerosis and end-organ damage. It is a stronger predictor of cardiovascular events and all-cause mortality than peripheral SBP. In particular, for children with congenital heart disease, a higher central SBP might impose a greater threat of cardiac damage. The aim of the study was to analyse and compare central SBP in children with congenital heart disease and in healthy counterparts. Patients and methods Central SBP was measured using an oscillometric method in 417 children (38.9% girls, 13.0 ± 3.2 years) with various congenital heart diseases between July 2014 and February 2017. The test results were compared with a recent healthy reference cohort of 1466 children (49.5% girls, 12.9 ± 2.5 years). Results After correction for several covariates in a general linear model, central SBP of children with congenital heart disease was significantly increased (congenital heart disease: 102.1 ± 10.2 vs. healthy reference cohort: 100.4 ± 8.6, p < .001). The analysis of congenital heart disease subgroups revealed higher central SBP in children with left heart obstructions (mean difference: 3.6 mmHg, p < .001), transpositions of the great arteries after arterial switch (mean difference: 2.2 mmHg, p = .017) and univentricular hearts after total cavopulmonary connection (mean difference: 2.1 mmHg, p = .015) compared with the reference. Conclusion Children with congenital heart disease have significantly higher central SBP compared with healthy peers, predisposing them to premature heart failure. Screening and long-term observations of central SBP in children with congenital heart disease seems warranted in order to evaluate the need for treatment.