Reduction of heart rate variability (HRV) parameters may be a risk factor and precede the occurrence of arrhythmias or the development of heart failure and complications in people with postinfarct left ventricular dysfunction and after coronary artery bypass grafting. Data on this issue in adults after a Fontan operation (FO) are scarce. This study assessed the association between HRV, exercise capacity, and multiorgan complications in adults after FO. Data were obtained from 30 FO patients (mean age 24 ± 5.4 years) and 30 healthy controls matched for age and sex. HRV was investigated in all patients by clinical examination, laboratory tests, echocardiography, a cardiopulmonary exercise test, and 24-h electrocardiogram. The HRV parameters were reduced in the FO group. Reduced HRV parameters were associated with patients’ age at the time of FO, time since surgery, impaired exercise capacity, chronotropic incompetence parameters, and multiorgan complications. Univariate analysis showed that saturated O2 at rest, percentage difference between adjacent NN intervals of >50 ms duration, and peak heart rate were associated with chronotropic index. Multivariable analysis revealed that all three variables were independent predictors of the chronotropic index. The results of this study suggest novel pathophysiological mechanisms that link HRV, physical performance, and organ damage in patients after FO.