Pandemics have presented new challenges for public transport organisers and operators. New diseases (e.g., influenza H1N1, severe acute respiratory syndrome—SARS, as well as, more recently, SARS-CoV-2) increase the need for new protection measures to prevent epidemic outbreaks in public transport infrastructure. The authors’ goal is to present a set of actions in the area of public transport that are adjusted to different levels of epidemic development. The goal goes back to the following question: how can the highest possible level of passenger safety be ensured and the losses suffered by urban public transport companies kept as low as possible? The sets of pro-active measures for selected epidemic scenarios presented in the article may offer support to local authorities and public transport operators. In the next steps, it is important to develop and implement tools for public transport management to ensure safety and tackle epidemic hazards.