Arrhythmias in patients with repaired tetralogy of Fallot (ToF) might be due in part to altered autonomic heart rate (HR) control caused by altered right ventricle hemodynamics. This study investigated autonomic HR control in ToF adolescents at rest and during unloading of the right ventricle. A total of 17 ToF patients and 56 healthy controls aged 12 to 18 years underwent orthostatic stress with lower body negative pressure (LBNP) of −20 mm Hg. HR, blood pressure and stroke volume were recorded non-invasively. Indices of HR variability were computed in time and frequency domains. All ToF patients also underwent cardiac magnetic resonance imaging, demonstrating pulmonary regurgitation and right ventricular dilation. At rest, HR variability indices of vagal heart rate control were non-significantly lower in the ToF patients compared to controls. During LBNP, HR increased more in controls than ToF patients (p ≤ 0.001). Further, most HR variability indices decreased among controls, but increased among ToF patients (p ≤ 0.01 or p ≤ 0.001 for all variables), suggesting vagal activation in the ToF patients. In conclusion, adolescents after ToF repair have fairly normal HR control at rest despite altered right ventricular hemodynamics. During unloading of the right ventricle, however, vagal HR control increases in the ToF patients and decreases in the controls.