A 5-year-old child experienced acute hemodynamic decompensation and hypoxia four weeks following an uneventful Fontan procedure for univentricular heart. Cardiac catheterization revealed complete occlusion of the left pulmonary artery, and emergent pulmonary artery embolectomy was performed. The source of the embolus was the atrial septal patch. Because of the altered hemodynamics following the Fontan procedure, stasis of right atrial blood and thrombus formation may occur. Routine anticoagulation immediately following operation is recommended. Prompt diagnosis and treatment with embolectomy may be lifesaving.