Introduction To investigate total annual precipitation, precipitation anomaly and aridity index in relation to linear growth in children under 5 in Uganda and quantify the mediating role of crop yield. Methods We analysed data of 5219 children under 5 years of age who participated in the 2016 Uganda Demographic and Health Survey. Annual crop yield in kilograms per hectare for 42 crops at a 0.1° (∼10 km at the equator) spatial resolution square grid was obtained from the International Food Policy Research Institute. Normalised rainfall anomaly and total precipitation were derived from the African Rainfall Estimation Algorithm Version 2 product. Linear regression models were used to associate total annual precipitation and anomalies with height-for-age z-scores and to explore the mediating role of crop yield qualitatively. The intervening effects were quantitatively estimated by causal mediation models. Results Twenty-nine per cent of children were stunted (95% CI 28% to 31%). After adjusting for major covariates, higher total annual precipitation was significantly associated with increasing height-for-age z-scores. At the mean, an increase of 1 standard deviation in local annual rainfall was associated with a 0.07-point higher z-score. Aridity index and precipitation anomaly were not associated with height-for-age z scores in altitude-adjusted models. Crop yields of nuts, seeds, cereals and pulses were significant mediating factors. For instance, 38% of the association between total annual precipitation with height-for-age z-scores can be attributed to the yield of sesame seeds. Conclusions Higher total annual precipitation at the village-level was significantly associated with higher height-for-age z-scores among children in Uganda. This association can be partially explained by higher crop yield, especially from seeds and nuts. This study suggests that more attention should be paid to villages with lower annual rainfall amounts to improve water availability for agriculture. ©