Children born with a functional single ventricle who undergo Fontan palliation are prone to early pump failure. Whether they develop early arterial stiffness with resultant increase in afterload is not well known. We hypothesized that the aortic stiffness is higher in pediatric Fontan patients when compared to healthy controls. A prospective study was conducted at the Children’s Hospital of Michigan. Twenty-two Fontan patients (aged 6–21 years) were compared with 22 healthy controls (aged 9–17 years) selected from children referred to our clinic who had normal cardiac anatomy and function on the echocardiogram. Aortic stiffness was assessed noninvasively by measuring the aortic augmentation index (AAI) using applanation tonometry (Sphygmocor, Atcor, IL). AAI was calculated as AP/PP where augmentation pressure (AP) is the increase in aortic systolic blood pressure (BP) and pulse pressure (PP) is the difference between aortic systolic and diastolic BP. Ten patients (45 %) had hypoplastic left ventricle, and 11 (50 %) had undergone aortic arch surgery. The median AAI was significantly higher in Fontan patients when compared to controls (12.5, IQR 4.8, 17.3 vs 0, IQR −6.3, 5.8; p = 0.0003). History of aortic arch surgery and single ventricle morphology did not have a significant impact on AAI. Pediatric patients who undergo Fontan palliation have significantly higher AAI, a marker of aortic stiffness and increased afterload, compared to healthy controls. Larger longitudinal studies are warranted to elucidate the possible contribution of elevated AAI on pump failure in these patients.