Management of patients with Eisenmenger syndrome with pulmonary atresia is challenging because of the complexity of the structure–function relationship of the components of the syndrome. Multi-modality imaging including cardiac magnetic resonance (CMR) 4D Flow offers unprecedented opportunities to unravel, at least in part, some of these components, and thus help in the management of these patients. In this study, we describe the use of these integrated methods with particular reference to CMR 4D Flow in a patient with Eisenmenger syndrome and pulmonary atresia and outline both the utility and the limitations. A comprehensive cardiac magnetic resonance (CMR) 4D Flow analysis was performed preoperatively and postoperatively, during peak systole, late systole, early diastole, and late diastole. The focus of the present study was to investigate the pattern of flow and dynamic changes at different levels of the aorta, as well as in the duct and the pulmonary arteries. Preoperatively, a right-handed helix and a vortex were observed in the dilated ascending aorta, and the duct flow was mainly dependent on reverse, upstream flow from the descending aorta, distal to the duct, during diastole, denoting low pulmonary vascular capacitance. Following repair, the flow in the ascending aorta and the descending aorta changed markedly. These changes included both timing and intensity of the right-handed helix, as well as the vortex in the ascending aorta. The significance of the observed changes in flow pattern and their influence on wall structure and function are discussed. Our study demonstrates the extremely powerful potential of CMR 4D Flow in the management of complex congenital anomalies.