Abstract This case report presents a rare benign salivary gland tumour called sialadenoma papilliferum. It comprises 3 to 5% of head and neck tumours and about 1% of all minor salivary gland tumours. The focus is on discussing the BRAFV600E mutation analysis and exploring its clinical implications, along with delving into the histopathological differentials. We documented a 73-year-old male, who had a white patch in the left retromolar trigone region for 6 months. The tumour was excised with a clinical diagnosis of verrucous lesion. Microscopic examination revealed exophytic hyperplastic parakeratotic stratified squamous epithelium and endophytic ductal papillary proliferation. The BRAFV600E mutation was present in the patient. Subsequent regular follow-ups were conducted, revealing no recurrence of the condition. This case underscores the pivotal role of BRAFV600E analysis as an invaluable diagnostic tool when confronted with the intricacies of intraoral salivary gland neoplasms.