Fast development and transmission of disease poses a health threat for a larger population and affects the functioning of almost all social systems, both within and outside nation-state borders, thus also affecting the possibilities of free migration and movement. The main aim of this article is to discuss the principal mechanisms of disease control in relation to migration in various socio-historical contexts. It identifies and compares historical patterns and contemporary measures of preventive control systems while considering the wider social context and migrants’ specific position. This paper combines the historical insights into various administrative and political systems in Europe and Croatia that have sought adequate measures to prevent the spread of infectious diseases with the current state of the affair in the fight against the COVID-19 pandemic. As part of the regulation and management of the contemporary COVID-19 pandemic, restrictions have been introduced on cross-border movement and travel. Those restrictions and quarantine measures have abruptly halted not only international but also migration within the borders of nation-states, especially during the first wave of the pandemic in spring 2020. Emphasis has been placed on the effects of the COVID-19 pandemic on labour and forced migration, as well as on the trends in public attitudes on immigrants affected by pandemic management mechanisms.