Herein, we report a case of a 27-year-old man with Ebstein’s anomaly and a history of unexplained recurrent venous thrombosis despite adequate anticoagulation. After surgical correction of the Ebstein’s anomaly, the venous thromboembolic events did not recur. This case demonstrates the possible etiopathogenesis of Ebstein’s anomaly in causing recurrent venous thromboembolism, which is likely caused through impedance of venous blood flow.Our objective in presenting this particular case is to highlight the possible association between Ebstein’s anomaly and venous thrombosis.