This article offers a critical analysis (both retrospective and prospective) of the dynamics of the development of legislation and judicial practice on the problem of the legal status of migrants with infectious diseases. There is an assessment of the proportionality (balancing) concerning the introduction of a state measure to limit the stay in the country and the deportation of migrants with infectious diseases (HIV, tuberculosis, and the coronavirus). The article focuses on the stages of development of the legal status of HIV-infected migrants’ in Russia under the influence of supranational judicial practice, as well as the difference in its application concerning other diseases. The article is intended to demonstrate how the potential of transnational regulation can be aimed at protecting human rights and freedoms in the current legal realities, and the developed legal mechanism can be implemented in law enforcement in case of emergencies in the health sector, including the spread of a pandemic.