The problem of organizing passenger transfers at regional airport hubs in terms of the pandemics is considered in the article. On the one hand, public transport has become a dangerous place for the spread of diseases. On the other hand, it is necessary for the existence of key sectors of the economy. A mathematical model of the synchronization of the arrival and departure of aircraft is proposed as the assignment problem. Unlike other available models, the goal is to slow down the speed of passenger flows with the ability to maintain social distance in the area of the transfer airport. The proposed model has a fan pattern schedule scheme, in which, until a certain estimated time, only arrival of vehicles is carried out and after this estimated time only departure. Aviation regional interchange hubs located in the Siberian part of the Russian Federation were considered in numerical experiments. To detail the restrictions, the service regulations for transit flights on domestic airlines were used. Thus, it is proposed to implement one of the concepts of transport operation in a pandemic, especially to abandon the speed as a service in favor of passengers’ safety.