Background: Malaria remains a public health concern and the leading cause of mortality in children aged under five years in South Sudan. Understanding the burden of malaria in children may assist in developing a strategy for mitigating and eliminating malaria. This would contribute to attaining the Sustainable Development Goals. We planned to determine the prevalence and outcome of malaria among hospitalized children in Al Sabah Children Hospital, South Sudan. Methods: We carried out a retrospective analysis of hospitalized children in Al Sabah Children Hospital between January to June 2020. The data for this study were analysed using Stata version 11 to calculate the prevalence and outcome of malaria among these children during the study period. Results: A total 781 children were recruited, of whom 777 contributed to the analysis (the others were excluded because of missing data). Overall prevalence of malaria was 78% among hospitalized children. Severe malaria alone affected 28%, while 50% had severe malaria in combination with other diseases. The highest death rate was amongst children from Munuki Block (11%, p= 0.001). Severe malaria alone and in combination was the diagnosis for 58% of the children who died. Severe malaria alone contributed to 14% of deaths. Conclusion: Malaria remains the number one cause of mortality in hospitalized children in this paediatric hospital. It predominantly affects young children, who are also at the highest risk of dying. Measures envisaged to protect children during their first five years of life are likely to have the greatest impact.