Introduction: The SARS-CoV-2/COVID-19 pandemic has triggered the need to develop rapidly effective and safe vaccines to prevent infection, particularly in those at-risk populations such as medical personnel. This study’s objective was to assess the perception of COVID-19 vaccination amongst Colombian physicians featuring two different scenarios of COVID-19 vaccination. Methods: A cross-sectional analytical study was carried out through an online survey directed at medical staff in several cities in Colombia. The percentage of physicians who have a positive perception to be vaccinated and the associated factors that determine that decision were determined. A binomial regression analysis adjusted for age and sex was carried out, taking as a dependent variable the acceptance of free vaccination with an effectiveness of 60 and 80%. The most significant factors were determined in the non-acceptance of vaccination. Results: Between 77.0% and 90.7% of physicians in Colombia accept COVID-19 vaccination, according to the scenario evaluated where the vaccine’s effectiveness was 60 or 80%, respectively. Medical specialty, having never paid for a vaccine, recommending the administration of the vaccine to their parents or people over 70 years, and dispensing the vaccine to their children, were the factors to consider to be vaccinated for free with an effectiveness of 60% and 80%. Conclusions: There is a high perception of the intention to vaccinate physicians in Colombia against COVID-19, and this is very similar to that of the general population.