Burundi’s high maternal and child mortality is caused in part by the high fertility rate, prompted by low rate of contraceptive use. Available sources report a contraceptive use of 18% among married women, but this excludes unmarried sexually active women. This study employed mixed methods to understand rates of contraceptive use in rural Burundi. We first assessed availability and uptake of contraceptives in 39 health clinics in the rural districts of Rumonge and Bururi. We selected sites with different utilization rates and conducted individual interviews and focus group discussions. 56 individuals participated including women, men, facility managers and community leaders. Uptake of family planning averaged 2.96%. Greater uptake was positively associated with the number of health professionals engaged and trained in family planning service provision as well as the number of different types of contraceptives available. Uptake was inversely associated with duration of stockouts and number of contraceptives stocked out. Qualitative data pointed to scarce resources, sociocultural factors, fear of disclosure and side effects, partner’s disapproval, and lack of information on modern contraceptives as explanations of low uptake. Interventions would need to take into account one or more of these factors in order to improve uptake of family planning