School enrolment has increased at an unprecedented scale in Sub-Saharan Africa but learning and the associated education efficiency have not. Given that resources are limited, the efficient use of inputs is of utmost importance for sustainable development. Hence, we investigate whether improvements in children’s nutrition can improve learning and hence efficiency. To assess this relationship, we employ average female height as our proxy for nutrition during childhood. For learning, we estimate numeracy and efficiency using a linearized version of the Whipple Index. Our data is at the subnational level focusing on the birth decades from 1950 to 1999. To deal with the endogeneity of nutrition, we use an instrumental variable approach. Our instrument is negative rainfall shocks during childhood which can adversely affect nutrition. We find that better nutrition increases education efficiency. Therefore, investments in nutrition can advance self-sustaining long-term growth based on human capital in Sub-Saharan Africa.