Few biomarkers for sepsis diagnosis are commonly used in neonatal sepsis. Whilst host response is increasingly recognized in sepsis pathogenesis and prognosis, there is a need for evaluating the accuracy of new biomarkers targeting host response in regions where sepsis burden is high and medico-economic resources are scarce. The objective of the study is to evaluate diagnostic and prognostic accuracy of biomarkers of neonatal sepsis in Sub Saharan Africa. This prospective multicentre study included newborn infants delivered in the Abomey-Calavi region in South Benin and their follow-up from birth to 3 months of age. Accuracy of transcriptional (CD74, CX3CR1), proteic (PCT, IL-6, IL-10, IP-10) biomarkers and clinical characteristics to diagnose and prognose neonatal sepsis were measured. At delivery, cord blood from all consecutive newborns were sampled and analysed, and infants were followed for a 12 weeks’ period. Five hundred and eighty-one newborns were enrolled. One hundred and seventy-two newborns developed neonatal sepsis (29.6%) and death occurred in forty-nine infants (8.4%). Among all tested biomarkers and clinical criteria, CD74/IP-10 ratio showed the best accuracy for neonatal sepsis diagnosis, while PCT accuracy was low. Among biomarkers and clinical criteria studied, only CD74 and PCT were independently associated with mortality, with CD74 showing an elevated predictive accuracy. These results suggest that cord blood PCT had a low accuracy for diagnosing early onset neonatal sepsis in Sub Saharan African neonates, while CD74/IP-10 ratio had the best diagnostic accuracy. CD74 expression at birth had the best accuracy in prognosing sepsis mortality.Trial registration: Clinicaltrial.gov registration number: NCT03780712. Registered 19 December 2018. Retrospectively registered.