The COVID-19 pandemic has had a significant impact on air transport in various parts of the world. The impact of the pandemic has been and still is significant within the Member States of the European Union. The introduction focused on identifying and monitoring the pandemic spread in the individual Member States. The research focused on two periods that were compared with each other based on key indicators, i.e., reproduction rate, hospitalized patients, or ICU patients. Identification and monitoring of the above-mentioned periods were performed by an observational study of collected data mentioned below. Subsequently, an algorithm was proposed, which was to determine an index number of a given country based on key indicators mentioned earlier. The index number is an assessment of the pandemic situation in a given country. The index number calculation in the monitored periods divided the countries into two groups: countries with the index number higher than one and countries with the index number lower than one. The latter can continue using air transport by pandemic situation assessment conducted by the algorithm. The air transport utilization rate depends on the second part of the algorithm, where the allowed number of routes is calculated for individual airlines. The use of an algorithm for calculating the index number of individual countries and at the same time monitoring the development of key indicators every 14 days is a suitable method for ensuring the sustainable use of air transport to minimize financial losses.