Inflammatory bowel disease (IBD) is rare in sub-Saharan Africa. Five cases in Nigerian children are presented to highlight the occurrence, pattern of clinical presentation and management challenges. The patients were identified following a retrospective review of all diagnosed cases of IBD between 1 January 2011 and 31 December 2018 seen at the Paediatric Gastroenterology, Hepatology and Nutrition Unit of Lagos State University Teaching Hospital. The median age (range) was 9 (7-13) years. Three cases were diagnosed because bloody diarrhoea persisted despite treatment at various health facilities for its common causes in the tropics and sub-tropics. The other two cases were confirmed after surgical intervention undertaken for symptoms of acute abdomen owing to appendicitis and intestinal obstruction. IBD should be considered in the differential diagnosis of children with chronic symptoms of bloody diarrhoea, weight loss, abdominal pain or abdominal masses.