We report the case of a 3-year-old girl who presented with near-lethal pulmonary thrombembolism 3 weeks after an uneventful Fontan operation. Complete occlusion of the left lower lobe pulmonary artery had occurred together with a cerebral infarction. Recombinant tissue plasminogen activator (rt-Pa) was used for thrombolysis because of its short half-life and its clot-selective properties. To further minimize the systemic effects of rt-PA, local catheter-directed lysis was performed. A prolonged course of low-dose rt-PA therapy achieved complete lysis without side effects.