Described herein is a 51-year-old woman with abdominal discomfort who was found to have a pericardial effusion and a large mass in her right heart by computed tomography scan and who then underwent tumour resection surgery. The tumour was so extensive that it involved the right atrium, the right ventricle and the tricuspid valve, and encompassed the right coronary artery. The patient had no significant medical history, and no tumour was found at any other site. The morphology of the tumour mimicked carcinosarcoma, exhibiting mixed epithelioid and spindle elements and it was difficult to differentiate the diagnosis even by immunohistochemical stains. Then, the final diagnosis of primary biphasic synovial sarcoma of the heart was established based on the finding of SS18 rearrangement. This is a highly intriguing rare case that may represent a diagnostic pitfall, particularly regarding frozen section. The patient will receive chemotherapy, and we will pursue follow-up.