Synovial sarcomas are rare malignant neoplasms arising from mesenchymal stem cells, comprising 8–10% of soft tissue sarcomas. One in three cases occur in those under 20 years old. The lower extremity and trunk are the most common sites, with less than 10% occurring within the head and neck region. They have a variety of clinical and radiological appearances, with occasional cystic degeneration. Here we present a case of a 9-year-old boy who presented with a presumed benign branchial cleft cyst seen on ultrasound and CT. A unilocular cyst was found adjacent to the lateral horn of the thyroid cartilage. When excised, the cyst was 4 cm with a variably thick wall of fleshy tissue containing straw-coloured fluid. Histologically, the cyst wall was composed of mitotically active spindle cells in fascicles separated by oedematous and collagenous stroma with occasional gland formation. Immunohistochemistry supported a diagnosis of synovial sarcoma, with positive epithelial membrane antigen (EMA), Bcl-2 and cytokeratin antigens, and was confirmed by fluorescence in situ hybridisation with a SS18 rearrangement. This case highlights the important consideration of malignant entities in common benign presentations.