Rice and wheat are the principal calorie sources for over a billion people in South Asia, although each crop is particularly sensitive to the climatic and agronomic management conditions under which they are grown. Season-long heat stress can reduce photosynthesis and accelerate senescence; if extreme heat stress is experienced during flowering, both rice and wheat may also experience decreased pollen viability and stigma deposition, leading to increased grain sterility. Where farmers are unable to implement within-season management adaptations, significant deviations from expected climatic conditions would affect crop growth, yield, and therefore have important implications for food security. The influence of climatic conditions on crop growth have been widely studied in growth chamber, greenhouse, and research station trials, although empirical evidence of the link between climatic variability and yield risk in farmers’ fields is comparatively scarce. Using data from 240 farm households, this paper responds to this gap and isolates the effects of agronomic management from climatic variability on rice and wheat yield risks in eight of Pakistan’s twelve agroecological zones. Using Just and Pope production functions, we tested for the effects of crop management practices and climatic conditions on yield and yield variability for each crop. Our results highlight important risks to farmers’ ability to obtain reliable yield levels for both crops. Despite variability in input use and crop management, we found evidence for the negative effect of both season-long and terminal heat stress, measured as the cumulative number of days during which crop growth occurred above critical thresholds, though wheat was considerably more sensitive than rice. Comparing variation in observed climatic parameters in the year of study to medium-term patterns, rice, and wheat yields were both negatively affected, indicative of production risk and of farmers’ limited capacity for within-season adaptation. Our findings suggest the importance of reviewing existing climate change adaptation policies that aim to increase cereal farmers’ resilience in Pakistan, and more broadly in South Asia. Potential agronomic and extension strategies are proposed for further investigation.