Mucoepidermoid cancer (MEC) is extremely rare in the palatine tonsil with only three adequately described cases in the literature.We describe a woman in her late 70s with vague pharyngeal discomfort who underwent tonsillectomy, lymph node dissection of the neck and radiotherapy for MEC with loco-regional lymph node metastasis of the palatine tonsil. To confirm this extremely rare diagnosis and to gain deeper insight in the molecular oncogenesis, an extensive molecular study including next-generation sequencing and immunohistochemistry was performed. Immunoreactivity for p16 protein and real-time PCR showed high-risk oncogenic human papillomavirus 16 DNA and mutations in the BRAF, BARD and DNMT3A genes. Tumour mutational burden was low. After a follow-up of 7 years the patient is still alive and well without any residual or disseminated disease.