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Background: Tuberculosis is a major public health problem worldwide. It can present in an acute form especially in endemic settings, which might lead to missed and delayed diagnosis, prolonged hospital stays, and increased mortality in children. South Sudan has a high prevalence of tuberculosis in the adult population. However, there is no published data on paediatric tuberculosis. We aimed to determine the prevalence and factors associated with pulmonary tuberculosis in children admitted with pneumonia in Al Sabah Children’s Hospital, South Sudan.Method: This was a cross sectional study of 404 children aged 2 to 59 months admitted with severe pneumonia from June-October 2018 at Al Sabah Children’s Hospital. We excluded children on anti-TB treatment. Data were collected using a pretested questionnaire which captured socio-demographic characteristics, clinical history, physical examination, and laboratory investigations. Sputum examination for Mycobacterium tuberculosis was performed for all participants using X-pert MTB/RIF. Additional investigations included Chest X-ray and blood count.Results: We recruited 404 children, out of which 78 (19.3%) had pulmonary tuberculosis. Of these, 13 (16.7%) were bacteriologically confirmed while 65 (83.3%) were clinically diagnosed. The factors significantly associated with pulmonary tuberculosis were age above two years [AOR 2.32 (95% CI 1.04-5.17)] p value 0.039, positive HIV Status [AOR 24.2 (95% CI 2.88-202.62)] p value 0.003, severe acute malnutrition [AOR 15.67 (95% CI 6.68-36.73)] p value <0.001, lack of BCG immunization [AOR 3.09 (95% CI 1.06-9.03)] p value 0.038, and contact with a known tuberculosis patient [AOR 55.14 (95% CI 10.12-300.6)] p value <0.001.Conclusion: There is a high burden of pulmonary tuberculosis in children presenting with severe pneumonia. There is a need for screening for pulmonary tuberculosis in children with any of the associated factors to improve early diagnosis and treatment.