Changing environmental conditions constitutes one of the greatest threats to human health by reducing agricultural yields and exacerbating the burden of undernutrition. Mozambique is a region characterized by a high dependence on agricultural productivity and an increasing prevalence of climate shocks in the form of droughts and floods. Low food availability as a result of changing environmental conditions can impair child development and long-term agricultural productivity, thus necessitating e!orts to understand and protect children’s health. Women’s empowerment is strongly associated with children’s nutritional status, such that disparities in maternal autonomy and educational attainment may explain variations in climate-related vulnerabilities in this regional context. The purpose of this research is to determine the extent climate shocks are associated with child undernutrition among di!erent populations in Mozambique by focusing on droughts and floods during the main crop growing season. In addition, this research investigates the potential of women's empowerment for mitigating climate-related vulnerabilities of children. Demographic health data is linked with regional gridded climate data using a stratified regression analysis to provide information on the impact of climate shocks on child undernutrition among livelihood subgroups of croppers and fishers. This cross-sectional study found that exposure to climate shocks during the main rainy season, from November to May, increases the risk of stunting in children under age five and that women’s empowerment may not be a mitigating factor in the protection of children’s health from climate shocks. Identifying population groups most adversely a!ected by climate change will be important for reducing social inequities and achieving the Sustainable Development Goals within Mozambique.