BackgroundFamily planning can reduce deaths, improve health, and facilitate economic development in resource-limited settings. Yet, modern contraceptive methods are often underused. This mixed-methods study, conducted in rural Burundi, sought to explain low uptake of contraceptives by identifying utilization barriers. Results may inform development of family planning interventions in Burundi and elsewhere.MethodsWe investigated uptake of contraceptives among women of reproductive age in two rural districts of Burundi, using an explanatory sequential, mixed-methods research design. We first assessed availability and utilization rates of modern contraceptives through a facility-based survey in 39 health clinics. Barriers to uptake of contraceptives were then explored through qualitative interviews (N = 10) and focus groups (N = 7).ResultsContraceptives were generally available in the 39 clinics studied, yet uptake of family planning averaged only 2.96%. Greater uptake was positively associated with the number of health professionals engaged and trained in family planning service provision, and with the number of different types of contraceptives available. Four uptake barriers were identified: (1) lack of providers to administer contraception, (2) lack of fit between available and preferred contraceptive methods, (3) a climate of fear surrounding contraceptive use, and (4) provider refusal to offer family planning services.ConclusionsWhere resources are scarce, availability of modern contraceptives alone will likely not ensure uptake. Interventions addressing multiple uptake barriers simultaneously have the greatest chance of success. In rural Burundi, examples are community distribution of contraceptive methods, public information campaigns, improved training for health professionals and community health workers, and strengthening of the health infrastructure.Electronic supplementary materialThe online version of this article (doi:10.1186/s12913-017-2144-0) contains supplementary material, which is available to authorized users.