The link between early childhood experiences and well-being in both childhood and adulthood has been reasonably well evidenced. Amongst the early childhood experiences, some developing country studies include weather shocks or seasonal variability as causal factors. We argue that such studies do not adequately capture shocks within seasons, or the intricate timing between agricultural harvests and milestones in early childhood development. Concentrating on the height-for-age z-scores of young Indonesian children, our model allows us to examine more closely the way in which rainfall variability, the timing of the rice harvest and infant weaning are linked. Our results suggest that children who are weaned at the end of the rice harvest in rural areas continue to be much healthier in childhood than those weaned at other times of the year, while in urban areas children are less healthy if they reach crawling age during the monsoon period. Contrary to other studies on Indonesia, we do not find any differences in health outcomes due to weather shocks by gender of the child.