A 49-year-old male presented to hospital with symptoms of acute cerebral infarction and pulmonary embolism who underwent transcatheter closure of atrial septal defect a year ago. Transthoracic echocardiography showed a 13×9 mm hypoechoic mass attached to the left-atrial side of the device, which was suspected to be 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 were 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.