This study examines the relationship between recent rainfall pattern and child nutritional outcomes in rural Madagascar. Using panel data at both individual and household levels, we assess both the direct and indirect effects of seasonal and annual precipitation on height-for-age z-scores (HAZ) and stunting, respectively. At the individual level, we find a positive association between moderate rainfall and improved HAZ. In contrast, both low and excessive rainfall during the rainy season are linked to adverse child growth outcomes. At the household level, such extremes may also disrupt agricultural production and household food consumption. We explore the indirect pathway through diet. Results show that rainfall variability significantly influences household dietary composition, including energy and protein intake from tubers—especially cassava—which play a central role in Malagasy rural diets. In the context of limited animal protein availability, tuber-derived protein contributes significantly to child growth, though it must be complemented by nutrient-dense foods to prevent protein-energy malnutrition. These findings highlight the need for climate-resilient agricultural strategies and diversified diets to strengthen food and nutrition security and improve child health outcomes in climate-vulnerable rural areas.