Background <p>The effect of vaccination on unrelated diseases, like the effect of influenza vaccination on COVID-19, has been shown in various studies. but the results of such studies are different and contradict each other. In Iran, not many studies have been done. The present study examines the relationship between Influenza vaccination and infecting with COVID-19.</p> Methods <p>The present study was conducted on a population of 3,000 individuals covered by the Iran University of Medical Sciences who had received COVID-19 vaccine before the start of study. This study was a retrospective cohort study. SPSS software (version 26) was used for data analysis. In order to estimate Hazard Ratio (HR), survival analysis and Cox regression model were used and, the relationship between Influenza vaccination and infecting with COVID-19 was investigated.</p> Results <p>The results of the study show that different levels of demographic variables such as occupation, education, underlying diseases, gender, age, exercise, and socio-economic status do not significantly increase or decrease the likelihood of COVID-19 infection. After adjusting for confounding variables, the calculated Hazard Ratio indicated that influenza vaccination has no significant effect on the outcome variable and is neither a risk factor nor a protective factor in the speed of COVID-19 infection (HR = 1.23, 95% CI: 0.819–1.859).</p> Conclusion <p>According to the results of study, Influenza vaccination is not a risk factor for infection with COVID-19. In a cohort study, it is not possible to adjust unknown and unexamined confounders, so in order to resolve possible ambiguities, more studies should be conducted in the future to adjust for such confounders.</p> Clinical trial number <p>Not applicable.</p>