A 5-year-old child with hypoplastic left heart syndrome presented with myocardial infarction 2 years after Fontan completion. Evaluation identified a thrombus in his native aortic root. Retrospective review of a prior catheterization revealed stasis in the native aortic root. Surgical thrombectomy was performed after failed medical management. The neoaortic root was revised at the time of thrombectomy in an attempt to reduce stasis in the native aortic root. This case suggests the need to identify anatomic findings that may predispose to coronary artery thrombus formation after Norwood palliation.