Synovial sarcoma (SS) is a rare soft tissue tumor, commonly arising in para-articular areas of extremities, but can also present in the head and neck area. However, primary SS of the thyroid gland is an extremely rare tumor which has been reported only five times in previous English literatures. This report presents fine needle aspiration (FNA) cytology of primary monophasic SS of the thyroid gland. A 47-year- old woman incidentally detected thyroid nodule in the isthmus of right thyroid gland on an ultrasonography by regular health check-up. Because the possibility of malignancy could not be ruled out, FNA and surgical resection were performed. The cytological, histopathological, immunohistochemical, and molecular genetic study of SYT-SSX transcript were discussed. For the past 3 years of follow-up after surgery, no recurrence or metastasis has been identified.