Background: Synovial sarcoma (SS) is a rare and aggressive entity that occurs predominantly in young adults. SS can arise in almost any part of the body, especially in the extremities. The incidence of SS in the parapharyngeal space is, however, quite low. Case presentation: Herein, we describe a case of a biphasic SS in the parapharyngeal space. A 22-year-old man presented with a pharyngeal foreign body sensation and underwent excision of the mass with a clear margin. Pathological examinations of the tumour specimen revealed a 1.7×1.5×1.2 cm spherical, well-circumscribed mass arising from the left side of the postpharyngeal wall. Histological examination showed a biphasic pattern of epithelioid and spindle cells, including glandular differentiation. Immunophenotype: Immunohistochemically, the tumour cells were positive for vimentin, and the spindle cells were positive for bcl-2; in contrast, the epithelioid tumour cells were positive for cytokeratin (CK) and epithelial membrane antigen (EMA) and weakly positive for CD99. The tumour cells were scattered positive for SMA. Thyroid transcription factor 1 (TTF-1), thyroglobulin (TG), p63, WT-1 and S100 were negative, and the proliferative index (Ki-67) was found in approximately 70% of the tumour cells. Then, the presence of the SYT-SSX gene fusion was demonstrated by fluorescence in situ hybridization (FISH). In addition, androgen receptor (AR) gene somatic mutations were detected by next-generation sequencing (NGS). Two months postoperatively, the patient had neither developed a recurrence nor received adjuvant radiotherapy and chemotherapy. Conclusions: Accurate diagnosis depends on morphological and immunohistochemical examination and a proper molecular analysis, and novel technologies can detect a wide variety of genetic alterations. The prognosis is relatively good in patients who undergo surgical resection with a clean margin.