Primary tracheal tumours are rare, comprising less than 1% of all airway malignancies. Amongst these, hyalinising clear cell carcinoma (HCCC) is an exceptionally uncommon entity. A low-grade malignant salivary gland tumour, HCCC most frequently arises in the minor salivary glands of the head and neck. We present a case of primary tracheal HCCC in a 47-year-old female, who was successfully managed with surgical resection and adjuvant radiotherapy. The patient’s primary complaint was 12 months of progressive dyspnoea and cough. Imaging studies, including a chest CT, revealed a 13x13x10mm lesion originating from the posterior tracheal wall. Bronchoscopy confirmed a pedunculated lesion obstructing more than 50% of the tracheal lumen. Histopathology, along with next-generation sequencing, identified a salivary gland neoplasm with an EWSR1-ATF1 fusion, confirming the diagnosis of HCCC. Following a multidisciplinary team review, the patient underwent a circumferential tracheal resection and primary end-to-end anastomosis. Postoperative care involved delayed extubation, followed by flexible bronchoscopy at 1 week for wound assessment and ultimately post operative radiotherapy. Hyalinising clear cell carcinoma is an uncommon salivary gland neoplasm, rarely presenting as a primary tracheal malignancy. This case highlights the challenges of diagnosing and managing primary tracheal HCCC, and details the surgical resection and primary closure technique.