The introduction of diphtheria immunisation into the Expanded Program of Immunisation in the 1970s has markedly reduced the incidence of diphtheria diseases. We report a case of fatal diphtheria in a 2 year-old girl whose immunisation status was not known. She had presented with acute exudative tonsillitis and was treated with intravenous amoxicillin-clavulanate but showed progressive signs of upper airway obstruction; stridor, drooling of saliva and bull-neck appearance, with bilateral facial swelling around the parotid region that extended to submental and submandibular regions. Initial cultures from blood, throat, nasal and oral cavity revealed no significant organisms. Corynebacterium diphtheriae subspecies gravis which was resistant to penicillin, was isolated from pus specimen a day after her demise. Clinical suspicion is important to aid diagnosis, microbiological confirmation and management of diphtheria, as the disease is rare in the era of successful immunisation programs. Microbiological vigilance plays an important role in early detection of infection as well as outbreaks. Early institution of diphtheria antitoxin may save lives, while delay in diagnosis may increase mortality and the risk of transmission. This case reaffirms the vital role of immunisation and the importance of efforts to ensure a high uptake of the scheduled immunisations.