We have reported the usefulness of the subxiphoid video-assisted thoracoscopic surgery approach in thymectomy. However, such a new method may have unknown complications that rarely occur. The brachiocephalic vein has been considered to be the vessel that is most frequently injured when performing thymectomy because of the skeletal anatomy. We herein report a case of intraoperative injury of brachiocephalic vein using tubeless subxiphoid thoracoscopic thymectomy. No additional complications have been found in the 3 months since the operation. Though subxiphoid video-assisted thoracoscopic surgery thymectomy is a safe and less invasive operation, intraoperative complications are possible, and surgeons should express caution.