In this study, through a cohort study of 10 million people, we investigated the association between estimated glomerular filtration rate (eGFR) and head and neck cancer (HNC) incidence. This is an observational cohort study using data from the national health claims database established by the Korean National Health Insurance Service (NHIS). We selected 9,598,085 participants older than 20 years who had undergone health checkups in 2009. A health checkup involves the history of any diseases, current health status, and results of several physical and blood exams including eGFR. We investigated the presence of HNC diagnosis in their national health insurance data from 2010 to 2018. Of the 9,598,085 participants, 10,732 had been newly diagnosed with HNC in the 9-year follow-up. In the multivariate Cox proportional hazard model, participants with elevated eGFR were associated with a risk of HNC incidence (HR = 1.129; 95% CI = 1.075–1.186 for eGFR = 90–104 mL/min/1.73 m2 and HR = 1.129; 95% CI = 1.076–1.194 for eGFR ≥ 105 mL/min/1.73 m2) compared with those with eGFR 60-89 mL/min/1.73 m2. Among HNC, the incidences of oral cavity, oropharyngeal, hypopharyngeal, and laryngeal cancers were significantly increased in the elevated eGFR group. According to the subgroup analysis, participants with eGFR ≥ 60 mL/min/1.73 m2 were correlated with risk of HNC incidence in middle age, non/mild drinker, low BMI, no diabetes, and no hypertension patients compared with those with eGFR < 60 mL/min/1.73 m2. Elevated eGFR was associated with the risk of some type of HNC, even in individuals with adjusted hypertension and diabetes without chronic diseases. The results of this study have implications for etiological investigations and preventive strategies.