In this report, a case of metaplastic thymoma arising in a thymic cyst wall is discussed. The patient was a 61-year-old male whose chief complaint was sweating and chest pain. Imaging study revealed a mediastinal mass with right hemithoracic extension. He underwent surgical resection of the mass and remnants of the thymus. Histologic studies showed a primary thymic neoplasm with a biphasic histologic pattern composed of 2 distinct epithelial and stromal components arising in a thymic cyst wall. Immunohistochemically, the epithelial component was cytokeratin positive and focally reactive for EMA. Marked expression of EMA and vimentin was seen in spindle cells. Metaplastic thymoma is an extremely rare variant of primary thymic epithelial neoplasms with only a few cases reported in the literature.