Given the aging population, use of an apicoaortic conduit serves as an alternative method to treat severe aortic stenosis, especially in patients with a heavily calcified ascending aorta or prior cardiac surgery. Although an apicoaortic conduit fractionates systemic blood flow, it does so without significant deleterious effects. However, we report a novel complication with thrombosis of the aortic root and subsequent coronary insufficiency that likely resulted from a preponderance of cardiac output though the apicoaortic conduit with stagnation of native antegrade blood flow. Given increasing use of the apicoaortic conduit procedure, surgeons considering this approach should be familiar with this potential complication.