A 24-year-old man known to have a double outlet right ventricle, status post-modified Fontan procedure at age 10, taking coumadin after having a stroke one year prior, presented with a massive pulmonary embolism and hemodynamic instability. Locally delivered tPA was unsuccessful, and the pulmonary artery thrombus was finally removed with a thrombectomy catheter (Angiojet thrombectomy); the patient recovered soon thereafter. This is the first report of the successful use of a thrombectomy catheter in a patient with pulmonary emboli and an occluded Fontan conduit.