The case report dealt with a rare case of thymic carcinoma arising from multilocular thymic cyst in a 59 year-old female. The peculiar presentation of tumor made clinical diagnosis of thymic origin impossible even after many sophisticated clinical studies, and pericardial effusion as a most likely diagnosis was suggested. The pathologic study of the specimen removed surgically revealed a multilocular thymic cyst with focal carcinomatous transformation in an area. The carcinoma had histological features of a basal cell carcinoma elsewhere. The clinical manifestation and pathogenesis of the tumor were fully discussed with relevant literature.