Primary pericardial synovial sarcoma is an extremely rare tumor. The awkward tumor site and clinical features associated with quite advanced disease at presentation make obtaining adequate biopsy material challenging. Ambiguous histologic features may also make diagnosis difficult. We present a case of a 15-year-old patient with an original diagnosis of a spindle cell thymoma. After definitive surgery the diagnosis was amended to a primary pericardial synovial sarcoma. Molecular confirmation of the SYT-SSX fusion gene was critical in reaching an accurate diagnosis. This highlights the necessity for routine molecular genetic studies, so that patient therapy can be directed accordingly.