Background: The TNM (tumor, node, metastasis) staging system is important for the successful treatment of head and neck cancers (HNCs). This study aimed to evaluate the concordance between clinical and pathological T and N stages in patients with HNCs in Poland. Methods: In this single-center retrospective study, clinical and pathological TNM staging data on 203 patients undergoing surgical treatment for HNC between 2011 and 2018 were collected and compared. The study group was classified as underdiagnosed, overdiagnosed, or correctly diagnosed with HNC based on pathological TNM staging. The concordance between clinical and pathological staging was evaluated using the kappa coefficient. Results: Clinical and pathological TNM staging showed concordance in 59.9% of patients for primary tumor (T) and in 79.3% of patients for lymph node (N) classifications. Moderate agreement between the clinical and pathological stages was shown for stage T, while substantial agreement was revealed for stage N. The size and extent of the tumor were underestimated or overestimated in 73 of the 182 patients (40.1%), while lymph node involvement was downstaged in 11 of the 53 patients (20.7%). Conclusions: The disparities between clinical and pathological staging of HNC demonstrate the need for standardization in physical and pathological examinations, as well as radiographic imaging.