Healthcare workers are at high risk of influenza virus infection as well as of transmitting the infection to vulnerable patients who may be at high risk of severe illness. The aim of this cross-sectional study was to investigate the prevalence and related factors of influenza vaccination coverage (2020–2021flu season), among members of the Athens Medical Association in Greece. This survey employed secondary analysis data from a questionnaire-based dataset on COVID-19 vaccination coverage and associated factors from surveyed doctors, registered within the largest medical association in Greece. All members were invited to participate in the anonymous online questionnaire-based survey over the period of 25 February to 13 March 2021. Finally, 1993 physicians (60% males; 40% females) participated in the study. Influenza vaccination coverage was estimated at 76%. Logistic regression analysis demonstrated that older age (OR = 1.02; 95% C.I. = 1.01–1.03), history of COVID-19 vaccination (OR = 2.71; 95% C.I. = 2.07–3.56) and perception that vaccines in general are safe (OR = 16.49; 95% C.I. = 4.51–60.25) were found to be independently associated factors with the likelihood of influenza vaccination coverage. Public health authorities should maximize efforts and undertake additional actions in order to increase the percentage of physicians/health care workers (HCWs) being immunized against influenza. The current COVID-19 pandemic offers an opportunity to focus on tailored initiatives and interventions aiming to improve the influenza vaccination coverage of HCWs in a spirit of synergy and cooperation.