Background: About 20 million children under fi-ve in Southern Africa have chronic malnutrition. This study determines the prevalence of chronic malnutrition and associated risk factors amongst children under five.Aim: To determine the proportion of children with chronic malnutrition and investigate associated risk factors of chronic malnutrition.Setting: The study was conducted in communities in the four regions of Eswatini.Methods: This study is a retrospective cross-sectional study that used data from a Multiple Indicator Cluster Survey (MICS) conducted in 2014. The study involved 3261 children who are under 5 years of age. Data on nutritional status and household characteristics were used. Logistic regression was used to identify factors associated with chronic malnutrition in the univariable and multivariable models, respectively.Results: Results showed that 18.1% (confidence interval [CI]: 18.5–21.5) of children under five have chronic malnutrition. The highest prevalence was 20.8% (CI: 17.4–24.7) in the Shiselweni region, followed by the Manzini region with 17.6% (CI: 14.5–21.1) and the Lubombo region with 17.2% (CI: 13.9–21.2). The lowest prevalence of chronic malnutrition at 16.7% (CI: 13.6–20.3) was the Hhohho region. The results indicated that low birth weight (odds ratio [OR] = 4.63, CI: 1.12–19.2), mothers’ lack of education (OR = 1.50, CI: 1.04–2.17) and children aged 12–24 months (OR = 1.28, CI: 0.88–1.87) were significantly associated with chronic malnutrition.Conclusion: The findings showed that malnutrition is an important public health problem in children under five and needs a multisectoral response. Low birth weight, mothers’ education and the child’s age are risk factors associated with chronic malnutrition.Contribution: The results inform evidence-based programming for the prevention of chronic malnutrition in children thus assist the country to meet sustainable development goals.