Healthy Flights Act of 2020 This bill provides authority for the Federal Aviation Administration (FAA) to impose any requirements on passenger and cargo air travel to protect the health and safety of air carrier crewmembers and passengers and to reduce the spread of such infectious disease through the aviation system during public health emergencies such as COVID-19 (i.e., coronavirus disease 2019). Among other provisions, the bill sets forth requirements relating to the use of masks and other protective equipment for airline passengers and certain airline employees; requires the FAA to provide certain employees, including any air traffic controller and airway transportation systems specialist, with masks and other protective equipment; mandates the development of a national aviation preparedness plan to ensure the aviation system is prepared to respond to epidemics and pandemics of infectious diseases; directs each air carrier operating an aircraft with a seating capacity of 20 or more to implement appropriate measures on a flight in air transportation for the purpose of reducing the likelihood of any passenger or crewmember contracting an infectious disease; requires the FAA to enter into an agreement with the National Academies to conduct a study on the transmission of infectious diseases, including airborne diseases, in the cabins of passenger airplanes; and establishes a Center of Excellence for Infectious Disease Response and Prevention in Aviation within the FAA.