A 49-year-old man presented to the hospital with symptoms of acute cerebral infarction and pulmonary embolism who underwent transcatheter closure of atrial septal defect a year before. Transthoracic echocardiography showed a 13 × 9 mm hypoechoic mass attached to the left-atrial side of the device, which was suspected to be a neoplasm or thrombus. The patient was indicated for surgery after multidisciplinary discussion due to ineffective medical therapy and typical stroke and pulmonary embolism symptoms. Three-dimensional transesophageal echocardiography (3D-TEE) revealed left-atrial vegetation (21 × 16 mm) and right-atrial vegetation (8 × 6 mm) attached to the device, which was confirmed as thrombus by surgical separation and laboratory examination. This case highlights the importance of 3D-TEE and a multidisciplinary team in the diagnosis and therapy of device-related thrombus.