We report a very rare case of a 38-year-old woman with an anomalous vein connecting the left atrium and superior vena cava. This vein originated from the roof of the left atrium and crossed the midline to join the normal right superior vena cava. Furthermore, there was no hypoplasia of the left heart, the atrial septum was intact, and all four pulmonary veins drained normally into the left atrium. Three-dimensional reconstructions and sagittal views on preoperative computed tomography clearly demonstrated a communication between the superior vena cava and the left atrium. The patient experienced increasing left-to-right shunt ratio and underwent successful surgical correction 3 years after the original diagnosis via ligation of the anomalous vein. This abnormal vein was considered to be a levoatrial cardinal vein. The embryology, physiology, diagnosis, and surgical repair of this rare lesion are discussed.