Background The nutritional well-being of infants and young children is influenced by economic, environmental and maternal factors that range from food intake, health, sanitation and care. All regions of Uganda have registered unacceptably high levels of childhood malnutrition over the years, although with an uneven distribution across regions. This study assessed health provider and caregiver perspectives on factors responsible for persistent malnutrition among children aged 0-59 months in Engaju and Nyakishana sub counties in Buhweju district.Methods In this phenomenological qualitative study, we conducted six Focus group discussions with Village Health Team members and care takers of children aged 0-59 months in Engaju and Nyakishana sub-counties and two key informant interviews with two members of the district health team to explore their perceptives on the factors responsible for persistent malnutrition in Buhweju District in May 2018. Data were thematically analyzed manually and using Atals Ti 7.5Results Historical and geographical challenges, poverty and economic occupation, parental alcoholism and domestic violence as well as inadequate childcare services were identified as factors responsible for persistent malnutrition among children aged 0-59 months in Engaju and Nyakishana sub counties in Buhweju district Conclusion Persistent malnutrition in children aged 0-59 months in Buhweju district is mainly due to historical and geographical challenges and its associated factors that include poverty and economic occupation, parental alcoholism and domestic violence and inadequate childcare services . Addressing these factors from the grassroots up through, multisectoral collaboration between infrastructure, Agriculture, Education and health, engaging communities and effective policy changes and implementation has the potential to improve the nutrition status of children in Buhweju district