This study determined with focus on gender disparity whether incidence based on age, tumor characteristics, patterns of care, and survival have changed in a population-based sample of 8288 German patients with head neck cancer (HNC) registered between 1996 and 2016 in Thuringia, a federal state in Germany. The average incidence was 26.13 ± 2.89 for men and 6.23 ± 1.11 per 100,000 population per year for women. The incidence peak for men was reached with 60–64 years (63.61 ± 9.37). Highest incidence in females was reached at ≥85 years (13.93 ± 5.87). Multimodal concepts increased over time (RR = 1.33, CI = 1.26 to 1.40). Median follow-up time was 29.10 months. Overall survival (OS) rate at 5 years was 48.5%. The multivariable analysis showed that male gender (Hazard ratio [HR] = 1.44; CI = 1.32 to 1.58), tumor subsite (worst hypopharyngeal cancer: HR = 1.32; CI = 1.19 to 1.47), and tumor stage (stage IV: HR = 3.40; CI = 3.01 to 3.85) but not the year of diagnosis (HR = 1.00; CI = 0.99 to 1.01) were independent risk factors for worse OS. Gender has an influence on incidence per age group and tumor subsite, and on treatment decision, especially in advanced stage and elderly HNC patients.