Because a persistent left superior vena cava (PLSVC) is a rare congenital malformation in the thoracic venous system, surgery of the thymus in such patients has rarely been reported. We herein present a case involving a 68-year-old woman who was treated for a thymic tumor adhering to a PLSVC. She underwent complete resection of the thymic tumor through median sternotomy with left-sided video-assisted thoracic surgery. Although the tumor was close to the left phrenic nerve, this nerve was safely preserved. The pathological diagnosis was mucosa-associated lymphoid tissue (MALT) lymphoma of the thymus. Thoracoscopy combined with median sternotomy enabled us to perform a safe surgical procedure for this patient.