Introduction Clinical and pathological staging plays an important role on the prognosis of head and neck cancer (HNC) patients. Objective The present study aims to compare clinical and pathological T, N and overall staging in patients with HNC, to identify factors associated with these discrepancies, and to analyze and compare survival or disease-free survival in staging disagreements. Methods Retrospective cohort including every patient submitted to neck dissection from January 2010 to December 2020 in the department of Otorhinolaryngology of a tertiary hospital center. Results A total of 79 patients were analyzed; their mean age was 58.52 ± 13.15 years old and 88.9% were male. Assessing overall staging, discrepancies were noted in 53% (36.4% upstaging and 16.6% downstaging) and were significantly associated with clinical overall staging ( p = 0.006). Regarding T staging, differences were noted in 45.5% (30.3% upstaging and 15.2% downstaging) and were significantly associated with imaging modality ( p = 0.016), clinical T staging ( p = 0.049), and histology ( p = 0.017). Discrepancies in N staging were noted in 38% (25.3% upstaging and 12.7% downstaging) and were significantly associated with age ( p = 0.013), clinical N staging ( p < 0.001), and presence of extranodal invasion ( p < 0.001). Both in Overall, T, and N staging, the aforementioned disagreements were not associated with either higher mortality or higher disease relapse. Conclusion Overall, T, and N staging disagree in an important number of cases, and the overall stage can disagree in up to 53% of the cases. These disagreements do not seem to influence overall and disease-free survival.