Synovial sarcoma (SS) is an uncommon malignant tumor associated with poor prognosis, and SS arising from the trachea is even rare with only three cases reported before. We present the case of a 19-year-old male and the imaging studies revealed a mass of soft tissue density in the lower trachea. An en bloc trachea segmental resection and post-operative proton beam therapy were performed. Diagnosis is confirmed by the SS18-SSX gene rearrangement. The patient is alive without tumor recurrence for 18 months. This is the first case of tracheal SS successfully treated with surgery and postoperative proton therapy.