Purpose Impact of COVID-19 pandemic on healthcare is huge. We intended to demonstrate how COVID-19 pandemic affected primary head and neck oncology patient's referral and admission to a tertiary center by comparing the retrospective patient data in March-September 2020 and the same period in 2019. Methods In this cross-sectional study, from March 15th, 2020 to September 15th, 2020, medical records of 61 patients (Group 1) diagnosed and scheduled for surgery for head and neck cancer in our tertiary care center were revised and compared with 64 head and neck cancer patients treated in the same institution in the same time period of the previous year (Group2). Surgical site, TNM stages, need for reconstruction with flap, time from first symptom occurrence to first admission to our institution, and time to surgery were noted. Results In Group 1, out of 56 patients, 26 were diagnosed with T1-2 tumor, while 30 had T3-4 tumor. In Group 2, 43 of 60 patients had T1-2 tumor, while only 17 of them were diagnosed with T3-4 tumor. The rate of T3-4 tumors had significantly increased in 2020 when compared to 2019 (p = 0.049). In oral cavity cancer patients, N stage was significantly increased in Group 1 when compared to Group 2 (p = 0.024). Need for reconstruction with regional or free flaps were significantly increased in oral cavity cancer patients (p = 0,022). The mean time from the beginning of the first symptom to the admission was 19.01 +/- 4.6 weeks (ranging between 11 and 32 weeks) in Group 1, while it was 16.6 +/- 5.9 weeks in Group 2 (ranging between 6 and18 weeks); with significant increase (p = 0,02). The time to surgery from first admission was 3.4 +/- 2.5 and 2.9 +/- 1.2 weeks in Group 1 and 2, respectively, with no statistically significant difference (p = 0.06). Conclusion The COVID-19 pandemic has caused delay in the diagnosis and treatment of many diseases as such in head and neck cancers. Admission with advanced stage disease and the need for more complex reconstructive procedures were increased. During the pandemic, the management of other diseases that cause mortality and morbidity should not be neglected and priorities should be determined.