The anomalous origin of the right pulmonary artery from the ascending aorta is a rare congenital anomaly usually diagnosed in infancy. When diagnosed later during adolescence, it presents diagnostic and treatment challenges, especially in determining whether pulmonary vascular disease can be reversed. We report the case of an 11-year-old girl who experienced increasing fatigue and was diagnosed with anomalous origin of the right pulmonary artery from the ascending aorta through echocardiography, CT angiography, and cardiac catheterisation. Segmental pulmonary hypertension was noted, but the operability was uncertain. A new non-invasive test combining 2D phase-contrast cardiac MRI with inhaled iloprost was performed. Flow measurements revealed a 42% rise in right pulmonary artery flow, indicating preserved vasoreactivity. Lung biopsy confirmed pulmonary vascular changes consistent with Heath–Edwards Stage II–III. Based on these findings, surgical reimplantation of the anomalous artery into the main pulmonary artery was performed. The postoperative recovery after surgery was uneventful, and follow-up catheterisation demonstrated normalised haemodynamics without residual stenosis. This case highlights the potential value of cardiac MRI–based vasoreactivity testing with inhaled iloprost as an additional tool alongside standard diagnostics for evaluating operability in late-presenting anomalous origin of the right pulmonary artery from the ascending aorta. Combining imaging, histopathology, and haemodynamic data allowed a personalised and safe surgical approach.