Background: Synovial sarcoma (SS) is a rare malignant soft tissue tumor. Primary intrathoracic SS is extremely rare, with limited diagnosis and treatment experiences. The aim of our study was to retrospectively study the clinicopathological characteristics, treatment and prognosis of primary intrathoracic SS and the impact of multidisciplinary team (MDT) management in diagnosis and treatment on patient prognosis. Methods: The clinical and pathological characteristics, treatment, survival and prognosis of patients with primary intrathoracic SS admitted to the National Cancer Center from January 1999 to December 2018, as well as MDT intervention during diagnosis and treatment, were retrospectively analyzed. Results: Thirteen patients were enrolled, including 7 (53.8%) males and 6 (46.3%) females, with primary intrathoracic SS in the lung (8/13, 61.5%), mediastinum (4/13, 30.8%) and pleura (1/13, 7.7%) as confirmed by morphological observation, immunohistochemical (IHC) staining and fluorescence in situ hybridization (FISH). Overall, 10/13 (76.9%) patients underwent surgery, and 6/10 (60.0%) received postoperative adjuvant therapy. Only 23.1% of patients received nonsurgical therapy. The MDT discussed and managed seven patients before and/or after surgery and one patient who did not undergo surgery. The estimated 3and 5-year overall survival (OS) rates were 50.0% and 30.0%, respectively. Patients who were managed by an MDT had a longer median OS time than those who were not (46.0 vs. 18.0 months). Age (P=0.018), tumor location (P=0.029), and Ki-67 (P=0.020) were found to be significantly related to OS.Conclusions: Monophasic morphology and fusion gene characteristics are the main features for the diagnosis of primary intrathoracic SS. MDT management can help obtain accurate diagnoses and provide reasonable therapeutic options.