We describe a case of patent ductus arteriosus (PDA) in a 76-year-old woman with a history of stroke, atrial fibrillation, and chronic obstructive pulmonary disease. Cranial diffusion-weighted imaging (DWI) performed for preoperative assessment showed a hyperintense lesion in the left cerebellum. Preoperative transesophageal echocardiography (TEE) demonstrated two highly mobile masses approximately 5 mm in diameter adherent to the left and non-coronary cusps of the aortic valve. We performed transpulmonary patch closure of PDA under hypothermic circulatory arrest. Subsequently, two frond-like masses were completely shaved off the cusps, preserving the native aortic leaflets. Pathological examination confirmed the diagnosis of papillary fibroelastoma (PFE). To our knowledge, this is the first report of PDA associated with PFE. Perioperative use of TEE is an effective tool for management of cardiovascular patients with suspected cardiogenic embolism.