Introduction: Tuberculosis is one of the most common causes of morbidity in children. Disseminated form causes more than one organ involvement, commonly seen in immune deficiency and malnutrition. Delay in diagnosis is due to paucibacillary nature and atypical presentation. Case presentation: 7-year-old boy from poor socio-economic background with severe malnutrition presented with chronic cough and fever for 3 weeks, associated with large joint arthritis. He was the second child of non-consanguineous parents with a healthy male sibling. He had a normal development and immunisation status, although protein energy malnutrition was present. He developed pancytopenia and high inflammatory markers with left lower zone consolidation.TB GeneXpert in repeated gastric aspirate became positive. Bone marrow biopsy and joint aspirates were normal. Child had incidental detection of hypogammaglobulinemia with absent CD19 cells. However, T cell function was normal with negative HIV screening. He responded to anti tuberculous treatment, intravenous immunoglobulins and meticulous nutrition optimisation with intense monitoring for refeeding syndrome. Joint arthritis responded to physiotherapy . Discussion: Cell-mediated immunity is crucial for containment of Tuberculosis. Malnutrition reduces expression of proinflammatory cytokines and maturation of T helper cells, causing secondary immune suppression. This leads to faster progression due to inefficient granuloma formation. Hypogammaglobulinemia has no direct effect on pathogenesis but increases the risk in a malnourished child. Diagnosis can be challenging in disseminated form and requires repeated clinical and laboratory evaluation. Poncet’s disease is a reactive polyarthritis seen as association in active Tuberculosis with negative synovial cultures. Early identification can prevent misdiagnosis.