Background <p>Head and neck cancers comprise multiple anatomical sites. Due to their rarity, previous studies have often aggregated anatomically or histologically distinct cancers or excluded rare entities altogether. Moreover, the list of head and neck cancer entities has evolved along with the adoption of new pathological insights.</p> Methods <p>In our previous study, we proposed a new classification of rare cancers, based on the International Classification of Diseases for Oncology 3.2 coding system, using data from cancer patients at all sites recorded in the National Cancer Registry of Japan. In this study, we created a comprehensive list of head and neck cancers to improve the accuracy of epidemiological reporting using population-based data from 2016 to 2019. Lymphoid diseases were excluded, and only epithelial tumors and sarcomas were included in the analysis.</p> Results <p>In Japan, head and neck cancer accounts for approximately 30,000 cases annually, accounting for 2.9% of all cancer cases. The incidence of squamous cell carcinoma arising from the oral cavity and lip was 7.5 cases per 100,000 per year, which does not meet the criterion for a rare cancer. Other head and neck cancers were rare. The most frequent sites were the oral cavity and lip, followed by the larynx, hypopharynx, and oropharynx. The annual number of cases increased during the study period.</p> Conclusion <p>Most head and neck cancers were rare during the study period. This result highlights the importance of continued efforts to track incidence trends in parallel with evolving pathological definitions.</p>