Mucosa-associated lymphoid tissue (MALT) lymphoma arising from the thymus is extremely rare. We present a case of a 23-year-old woman with systemic lupus erythematosus (SLE) who was diagnosed with thymic MALT lymphoma. In 2004, she was diagnosed with a mediastinal tumor on chest radiography during medical follow up for SLE. An anterior mediastinal tumor with multilobular cysts was identified by computerized tomography and magnetic resonance imaging. A thymic malignancy was suspected and an extended thymectomy was performed. After histological and immunohistochemical examinations, the thymic tumor was diagnosed as a MALT lymphoma. There was no recurrence in the 2-year follow-up during which time there was no further treatment.