Thrombus formation in a pulmonary vein stump after pulmonary lobectomy is extremely rare, but can trigger cerebral embolism of unknown cause. We encountered a case of cerebral embolism in a 58-year-old man 2 days after left upper lobectomy. Since intravenous administration of recombinant tissue plasminogen activator was contraindicated, thrombus removal by endovascular reperfusion therapy was performed. Cerebral angiography showed left internal carotid artery occlusion. Thrombus removal using a retrieval device was performed and complete recanalization of the left internal carotid artery was obtained. Although blood abnormalities or arrhythmia such as atrial fibrillation were not observed, thrombus in the left upper pulmonary vein stump was detected with contrast-enhanced computed tomography of the body trunk, which was therefore considered as the source of cerebral embolism. The patient is continuing on anticoagulant therapy to prevent embolism recurrence caused by thrombus formation in the pulmonary vein resection stump. To the best of our knowledge, this is the first report of thrombus removal by acute-phase endovascular reperfusion therapy to treat cerebral embolism likely caused by thrombus formation in the pulmonary vein stump after left upper lobectomy. When cerebral embolism of unknown cause develops after left upper lobectomy, thrombus formation in the pulmonary vein stump should be considered among the differential diagnoses. For acute-phase onset of cerebral embolism after pulmonary lobectomy, thrombus removal by endovascular reperfusion therapy may be considered as one of the therapies.