This study explored the challenges in establishing a mortuary-based injury surveillance system in a resource-constrained setting of Ibadan, Nigeria. To quantify and detail fatal injuries, in September 2010 to February 2011, a prospective data collection utilised the World Health Organization-Monash draft surveillance system. Findings were compared with other low- and middle-income settings, and surveillance system attributes were assessed. The leading injury mechanism among all age groups was transport related, with 45.6% being vulnerable road users, consistent with comparable settings. Fire-related injury was the second unintentional cause in the Ibadan pilot, unlike Global Burden of Disease estimates for Nigeria, Mauritius and Mexico, where drowning was the second cause. Positive system attributes included timeliness, data field completeness, specificity, flexibility and sensitivity. Despite apparent under-reporting of eligible deaths and questionable representativeness, this study illustrates potential for mortuary data to inform injury prevention policies and programmes in resource-constrained settings.