A 42-year-old Japanese woman complained of upper abdominal pain. Endoscopic examination demonstrated an elevated lesion in the body of the stomach, and a biopsy specimen demonstrated proliferation of atypical spindle cells. She underwent partial gastrectomy; the resected tumor measured 3.5 × 2.8 × 1.2 cm in size. Histological examination disclosed the haphazard proliferation of spindle cells in the mucosa mixed with less prominent epithelioglandular component. The spindle cells were positive for cytokeratin, vimentin, EMA and CD99, but not for KIT, DOG1, desmin or S100. Reverse transcription-polymerase chain reaction using paraffin sections amplified a SYT-SSX1 chimera transcript. A diagnosis of synovial sarcoma was made. There has been no sign of recurrence or metastasis for 6 years after the operation. Synovial sarcoma in the stomach is very rare. Since differential diagnosis of synovial sarcoma from carcinosarcoma and mesenchymal tumors is critical for the treatment and prediction of prognosis, accurate diagnosis with molecular analysis is essential.