Anomalous drainage of the right superior caval vein into the left atrium is a rare congenital anomaly that causes cyanosis and occult infection owing to right-to-left shunting. Transcatheter management of this anomaly is unique and rarely reported. We report a 32-year-old man with a history of brain abscess, who was diagnosed with an anomalous right superior caval vein draining to the left atrium; right upper pulmonary vein and right middle pulmonary vein draining into the inferior portion of the right superior caval vein; and a left superior caval vein draining into the right atrium through the coronary sinus without a bridging vein. Pre-procedural planning was guided by three-dimensional printed model. The right superior caval vein was occluded with a 16-mm Amplatzer muscular Ventricular Septal Defect occluder inferior to the azygous vein, but superior to the entries of right upper and middle pulmonary veins. This diverted the right superior caval vein flow to the inferior caval vein system through the azygos vein in a retrograde manner and allowed the right upper pulmonary vein and right middle pulmonary vein flow to drain into the left atrium normally, achieving exclusion of right-to-left shunting and allowing normal drainage of pulmonary veins into the left atrium. At the 6-month follow-up, his saturation improved from 93 to 97% with no symptoms of superior caval vein syndrome.