A 67 years old male had underwent left upper division segmentectomy. On the sixth day after surgery, he had developed unconsciousness, aphasia and unilateral spatial neglect. Brain MRI revealed a cerebral infarction, and percutaneous cerebral thrombectomy was performed. Enhanced computed tomography revealed thrombus formation in the remnant superior pulmonary vein (SPV), left renal infarction and right acute limb ischemia. After starting anticoagulant therapy with apixaban the thrombus reduced and neurological symptoms improved. A thrombus in the SPV may cause serious whole body organ infarction in the same way as a left atrial thrombus. It was suggested that left upper division segmentectomy was associated with the risk of remnant pulmonary vein thrombosis.