Advances in head and neck cancer (HNC) treatment might have changed treatment strategies. This study determined, with focus on gender disparity, whether treatment rates have changed for inpatients in Germany between 2005 and 2018. Nation-wide population-based diagnosis-related groups (DRG) data of virtually all HNC cases (1,226,856 procedures; 78% men) were evaluated. Poisson regression analyses were used to study changes of annual treatment rates per German population. For surgery, the highest increase was seen for women with cancer of the oral cavity (relative risk (RR) 1.14, 95% confidence interval (CI) 1.11–1.18, p < 0.0001) and the highest decrease for men with laryngeal cancer (RR 0.90, CI 0.87–0.93). In women with oropharyngeal cancer, the highest increase of radiotherapy rates was seen (RR 1.18, CI 1.10–1.27, p < 0.0001). A decrease was seen in men for hypopharyngeal cancer (RR 0.93, CI 0.87–0.98, p = 0.0093). The highest increase for chemotherapy/immunotherapy was seen for women with oropharyngeal cancer (RR 1.16, CI 1.08–1.24, p < 0.0001), and a decrease in men with hypopharyngeal cancer (RR 0.93, CI 0.88–0.97, p = 0.0014). Treatment patterns had changed for nearly all subsites and therapy types. There were relevant gender disparities, which cannot be explained by the DRG data.