Background: Undernutrition may become the most significant impact of climate change on child health, especially in subsistence farming populations, because of adverse effects of changes in weather patterns on crop yields and consequent undernutrition-related morbidity and mortality. However, empirical evidence is limited. Aim: To examine crop yield variation as a risk factor for child undernutrition and mortality in the context of weather variability in a subsistence farming population of rural Burkina Faso. Methods: Epidemiological analyses in the Nouna Health and Demographic Surveillance System of: (1) the association of child Middle-Upper Arm Circumference (MUAC) with crop harvest and annual yield variation, and (2) associations of child survival with annual crop yield variation and with MUAC. Analysis of observed weather–crop yield associations was used to predict future yields and child mortality attributable to annual yield reductions using daily weather data from global climate models that assume 1.5°C global warming by 2100. Results: There was evidence that lower household crop harvests are associated with reduced MUAC, and annual yield reductions with both smaller MUAC and poorer child survival (hazard ratio for mortality of 1.11 (95% CI 1.02, 1.20) for a 90th–10th centile decrease in yield). Burden estimates suggest that low crop yields account for 7 child deaths per year in a population of 100,000 people of all ages under the current weather conditions, and a larger burden under trajectories consistent with 1.5°C global warming by 2100. Conclusion: I found evidence of crop yield variation as a risk factor for child undernutrition and mortality in a subsistence farming population of rural Burkina Faso. The impact of such variation is likely to be exacerbated under climate change. This evidence strengthens the case for protection of child nutrition and health by addressing crop yield deficits in the context of weather and climate variability.