Many autoimmune diseases have been reported to be associated with malignancy. Mixed connective tissue disease (MCTD), however, has rarely been associated with malignancy. Thymoma is one of the neoplasms often reported to be related to various immunological disorders. Among the types of thymoma defined by WHO, malignant thymoma (thymoma type C) is the one least reported to be associated with autoimmune disease. Here, we report a case of malignant thymoma with concurrent MCTD, which manifested with acrosclerosis, Raynaud's phenomenon, arthritis (synovitis), and a high titer of anti-ribonucleoprotein antibody.