Typhoid is an acute febrile illness primarily caused by Salmonella enterica serotype typhi (S. Typhi) which could be challenging to diagnose in children, owing to its non-specific clinical signs and symptoms which may resemble other febrile illnesses. Here, we present a case of typhoid which was atypically presented as fever of unknown origin (FUO) in a two-year-old boy with underlying glucose-6-phosphate dehydrogenase (G6PD) deficiency. This child was initially diagnosed and managed as acute tonsillopharyngitis, however remained febrile despite medications. A series of investigations were performed and S. Typhi was isolated from the bone marrow culture after almost a month of admission. The antibiotic was started based on antibiotic susceptibility testing and he recovered well. Our case underscores the challenges of diagnosis establishment and clinical management of typhoid in paediatric patients who has underlying disease and emphasizes the importance of having high index of clinical suspicion to ascertain timely and proper diagnosis.