Although huge advances have been made in the field of medicine, fever of unknown origin (FUO) continues to be a significant health problem and an important cause of morbidity and mortality, especially in children. The aim of this study was to study current spectrum of FUO, newly emerging challenges and outcome of FUO. A prospective observational study was conducted over a 16 month period (May 2012-September 2013). 53 children aged 4 months to 15 years met the definition of FUO and were included. Children with known immunodeficiency disorders or other chronic disorders were excluded. A diagnosis was reached in 47 (88.7%) patients. Infections were the commonest cause accounting for FUO in 37 (69.8%) patients. Haematological disorders were found in 8 (15%) and autoimmune diseases in 2 (3.8%) patients. Among infections, the most common causes of FUO were tuberculosis (TB) (37.8%), enteric fever (29.7%), Epstein-Barr virus (EBV) (8.1%) and brucellosis (8.1%). TB was extra-pulmonary in 11 cases and pulmonary in 3 cases. Amongst the haematological disorders, 3 patients had haemophagocytic lymphohistiocytosis (HLH), 3 had leukemia, 1 had non-Hodgkin lymphoma and 1 had autoimmune lymphoproliferative syndrome. Juvenile idiopathic arthritis with systemic onset and polyarteritis nodosa accounted for the two cases of autoimmune disease. Elevated C-reactive protein (CRP) levels were associated with an infectious etiology. Bone tenderness, thrombocytopenia and neutropenia predicted haematological malignancy. 1 patient of HLH died of complications during initial hospitalization and 3 other patients (1 HIV, 2 TB) died on follow up. TB, especially extrapulmonary, and enteric fever are still significant public health problems and were the commonest causes of FUO in our population. Due to advances in diagnostic facilities, some diseases like urinary tract infection (UTI) and hepatitis have become less common; however, other diseases like EBV have become more common causes of FUO. HLH is emerging as a significant cause of morbidity and mortality in FUO patients.