Pharyngitis is one of the manifestations of SARS-CoV-2 infection, which features specific changes in the pharyngoscopic pattern, long fluctuating course and increase in symptoms severity after a physical exercise, which requires long-term therapy with topical agents. A comparative analysis of Tonsilgon N effect on the course of SARS-CoV-2 associated pharyngitis as well as post-COVID syndrome development was carried out in this study. 164 patients with acute pharyngitis associated with SARS-CoV-2 were included in the study. Main group (n=81) received Tonsilgon N oral drops in addition to the standard treatment regimens for pharyngitis and control group (n=83) received standard regimen alone. Treatment regimen lasted for 21 days for both groups, followed by follow up examination in 12 weeks for assessment of post-COVID syndrome development. Patients taking Tonsilgon N showed a statistically significant symptoms improvement in throat pain relief (p=0.002) and throat discomfort (p=0.004), however, no statistically significant difference in two groups were observed in inflammation severity based on pharyngoscopy examination (p=0.558). Addition of Tolzilgon N to the regimen reduced occurrence of secondary bacterial infections and therefore use of antibiotics more than 2.8 times (p<0.001). Compared with the control group long term topical therapy with Tolzilgon N showed no increase in occurrence of side effects such as allergic reactions (p=0.311) as well as subjective burning sensations in the throat (p=0.849). In main group occurrence of post-COVID syndrome was observed 3.6 times less than in the control group (7.2% vs 25.9%, p=0.001). These results give us the ground for indication of Tonsilgon N use in the treatment of viral pharyngitis associated with SARS-CoV 2 infection and in prevention of post-COVID syndrome.