Atresia of the coronary sinus (ACS) is a rare congenital anomaly. When associated with persistent left superior vena cava (PLSVC), this defect could have no significant hemodynamic effect, and the patient might remain asymptomatic. However, vascular interventions might induce changes or complications that could show the anomaly. Appropriate management requires a good understanding of this condition. We present the first reported case of ACS and PLSVC occurring after thrombosis of the innominate vein (IV) after central venous catheter placement. The patient presented with atypical subacute chest pain and recurrent extrasystoles. Diagnosis and characterization of vascular anomalies was made by computed tomography phlebography, and the patient was successfully managed by endovascular recanalization of the IV.