We report a rare case of a pulmonary vein stump thrombus detected by a contrast-enhanced computed tomography for transient syncope 2 days after upper division segmentectomy of the left lung for metastatic pulmonary tumor. The thrombus disappeared without embolic events after anticoagulation with intravenous heparin followed by oral warfarin. Considering this case and previous reports, thoracic surgeons should be aware of pulmonary vein stump thrombus, a latent source of systemic embolization, after pulmonary resection, especially lobectomy or segmentectomy of the left upper lobe. This possible serious complication can occur at any time from the early postoperative period.