Synovial sarcoma (SS) is a mesenchymal tumour of uncertain histiogenesis that can show dual epithelial and mesenchymal differentiation. Thought to arise predominantly in deep soft tissue of extremities, these sarcomas have shown that they can affect a wide variety of organs and sites, however intraoral mucosal SS is rarely encountered and herein the authors present possibly the second reported case of a young lady presenting with a slow growing tumour arising in the gingivo-buccal sulcus that was reported as Synovial sarcoma on biopsy and subsequently confirmed using molecular studies, tumour demonstrating SS18-SSX2 fusion transcript. Review of the published literature revealed no documented case with molecular fusion transcript making this case the first reported case. This case also highlights the imperative role of immunohistochemistry in tandem with molecular studies to confirm the diagnosis of spindle cell tumours of oral cavity, since squamous cell carcinoma, by far remains the commonest malignancy arising in mucosa lined oral cavity.