DHFR 19-pb ins/del (rs70991108) was associated with a protective effect against HNSCC development compared to the C group by the codominant (OR = 0.42; 95% CI = 0.27–0.65; p < 0.001), dominant (OR = 0.48; 95% CI = 0.32–0.73; p < 0.001), and overdominant models (OR = 0.48; 95% CI = 0.32–0.71; p < 0.001). Here, DHFR is linked to head and neck squamous cell carcinoma.