BACKGROUND: Malnutrition is a critical public health concern in South Sudan where an estimated 200,000 children aged under five years are at risk of being malnourished. Studies have shown that adequate and timely treatment of these children leads to reduced mortality. OBJECTIVE: To determine the proportion of children aged 6 – 59 months diagnosed with severe acute malnutrition (SAM) who were appropriately managed according to World Health Organization (WHO) guidelines. METHODS: A short hospital-based prospective longitudinal survey of children admitted with a diagnosis of SAM to Al Sabah hospital, Juba. One hundred children were enrolled. RESULTS: Overall, 49% of children had marasmus and tended to be older than those who had kwashiorkor. Common comorbidities at admission were malaria (42%) and gastroenteritis (39%). Of the eight steps of care evaluated, five steps were correctly followed in more than 70% of cases. The proportion of children appropriately managed were 77% in step 1, 59% in step 2, 85.4% in step 3, 98% in step 4, 58% in step 5, 6. 97% in step 7 and 86% in step 8. CONCLUSION: Adherence to the WHO guidelines for treating SAM in this center was moderate.