Significance The recent increase in large-scale migration trends generates several concerns about public health in destination countries, especially in the presence of massive incoming human flows from countries with a disrupted healthcare system. Here, we analyze the flow of 3.5 M Syrian refugees toward Turkey to quantify the risk of measles outbreaks. Our results suggest that heterogeneity in immunity, population distribution, and human-mobility flows is mostly responsible for such a risk: In fact, adequate policies of social integration and vaccine campaigns provide the most effective strategies to reduce measles disease risks for both migrant and hosting populations.