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Under-five child mortality declined 47% since 2000 following the implementation of the United Nation’s (UN) Millennium Development Goals. To further reduce under-five child mortality, the UN’s Sustainable Development Goals (SDGs) will focus on interventions to address neonatal mortality, a major contributor of under-five mortality. The African region has the highest neonatal mortality rate (28.0 per 1000 live births), followed by that of the Eastern Mediterranean (26.6) and South-East Asia (24.3). This study used the Demographic and Health Survey Birth Recode data (http://dhsprogram.com/data/File-Types-and-Names.cfm) to identify high-risk districts and countries for neonatal mortality in two sub-regions of Africa – East Africa and West Africa. Geographically weighted Poisson regression models were estimated to capture the spatially varying relationships between neonatal mortality and dimensions of potential need i) care around the time of delivery, ii) maternal education, and iii) women’s empowerment. In East Africa, neonatal mortality was significantly associated with home births, mothers without an education and mothers whose husbands decided on contraceptive practices, controlling for rural residency. In West Africa, neonatal mortality was also significantly associated with home births, mothers with a primary education and mothers who did not want or plan their last child. Importantly, neonatal mortality associated with home deliveries were explained by maternal exposure to unprotected water sources in East Africa and older maternal age and female sex of infants in West Africa. Future SDG-interventions may target these dimensions of need in priority high-risk districts and countries, to further reduce the burden of neonatal mortality in Africa.