Hunger and malnutrition are rampant among refugees and displaced populations, many of whom are infants and children. We sought to determine the prevalence and factors associated with thinness among children aged 5–17 years living in Nakivale refugee settlement, Isingiro district, southwestern Uganda. This was a cross sectional study that enrolled 420 children aged 5 to 17 years. The World Health Organization cluster sampling was used to select 30 villages from which 14 households were selected by consecutive sampling and participants were then chosen per household by simple random sampling. Data were collected on the participant socio-demographic, family, dietary, medical, hygiene and refugee status factors. Thinness was defined as having a z-score < -2 standard deviations of Body Mass Index-for-age from the median WHO growth standards. The prevalence of thinness was determined by ascertaining the total number of children with thinness over the total number of children stu