question: Based on the authors’ work in Latin America and Africa, this article describes and applies the concept ‘structural vulnerability’ to the challenges of clinical care and healthcare advocacy for migrants. This concept helps consider how specific social, economic and political hierarchies and policies produce and pattern poor health in two case studies: one at the USA–Mexico border and another in Djibouti. Migrants’ and providers’ various entanglements within inequitable and sometimes violent global migration systems can produce shared structural vulnerabilities that then differentially affect health and other outcomes. In response, we argue providers require specialised training and support; professional associations, healthcare institutions, universities and humanitarian organisations should work to end the criminalisation of medical and humanitarian assistance to migrants; migrants should help lead efforts to reform medical and humanitarian interventions; and alternative care models in Global South to address the structural vulnerabilities inherent to migration and asylum should be supported.