The majority of research on linear growth among children is confined to South Asia and focuses on iron and folic acid (IFA) supplementation during pregnancy, without considering malaria prophylaxis. Similarly, there is limited evidence on the association of antenatal IFA supplementation and malaria prophylaxis with neonatal mortality in sub-Saharan Africa (SSA). This study aims to address these gaps. A pooled analysis of demographic and health survey (DHS) data from 19 countries in SSA was conducted to study the association between IFA supplementation and malaria prophylaxis and linear growth and neonatal mortality. Multivariate logistic and linear regression models were used. Malaria prophylaxis was significantly associated with stunting, height-for-age Z scores (HAZ scores), and neonatal mortality, but IFA supplementation was not associated with these outcomes. When women’s height and body mass index (BMI) were introduced in the model, a significant association between combined malaria prophylaxis and IFA supplementation was found with HAZ scores only. For severe stunting, no significant association was found with either in the two models. In conclusion, this study underscores the importance of antenatal malaria prophylaxis as a potential intervention for nutrition outcomes (linear growth) and neonatal mortality, as well as the importance of coordinating efforts between malaria and the health and nutrition sectors to improve these outcomes in the countries of SSA.