The disease COVID-19 negatively affected sustainable mobility, including public passenger transport, as it was necessary to take several measures to reduce the population’s mobility. It also limited rail passenger transport. Railway operators suffered from a significantly reduced number of passengers. An analysis of the transport performance of railway passenger transport is conducted in a case study in Slovakia. Based on the decline in transport performance in railway passenger transport and the degree of measures introduced, a new methodology and procedure for introducing pandemic measures are proposed in the context of reducing the scope of rail passenger transport. The measures are proposed under the condition that it is necessary to monitor the roles and responsibilities of railway infrastructure managers and rail passenger operators. The proposed methodology includes a transport performance forecast according to the defined transport reduction measure level and the train traffic diagram variants on the model railway line in the case of levels of the implemented measures. These proposals will contribute to higher quality and more efficient railway transportation, including optimal use of railway infrastructure capacity during emergency situations. The novelty of the research lies in the new methodological procedure and its practical application.