Objectives <p>Substantial inequalities in access to healthcare are common in rural and marginalized populations in the Global South, and these inequalities can drive health disparities. Historical mistrust of healthcare institutions can further impact healthcare behaviors, including vaccination. Here, we apply the concept of medical mistrust, which has been widely applied to healthcare decisions in industrialized countries, across a rural–urban spectrum of communities in Namibia, and assess its utility in understanding vaccination decisions.</p> Methods <p>Otjiherero-speaking indigenous communities of Kunene, Namibia, were surveyed to assess medical mistrust. Participants also answered questions about COVID-19 vaccination status, vaccine safety, and interest in a hypothetical malaria vaccine. Bayesian multilevel models were used to compare medical mistrust across communities and its influence on vaccination and vaccine perceptions.</p> Results <p>The level of medical mistrust varied across contexts, with the highest level of mistrust in peri-urban communities. Medical mistrust predicted beliefs about vaccine safety and interest in the malaria vaccine, but not COVID-19 vaccine status, which was largely driven by access to the vaccine. For rural and peri-urban Himba, participants also expressed disinterest in the COVID-19 vaccine and worries about its safety.</p> Conclusion <p>Addressing global health disparities requires understanding how locally contextualized social and ecological experiences shape healthcare and vaccination decisions. Results of this study show fundamental differences in medical mistrust by community, which may be contributing to beliefs about vaccines. Understanding how medical mistrust varies across these contexts, and how it impacts perceptions about vaccination, can inform health communication and public policy in underserved communities.</p>