Flood, a natural disaster closely related to global climate change, harms child health. However, the long-term effect of flood exposure on child mortality is unknown, particularly in low- and middle-income countries (LMICs). Here, based on a sibling-matched case-control design and exposure data of 913 large flood events, we first estimate the under-5 deaths (U5Ds) attributable to long-term flood exposure in 100 LMICs, where there are >90% of global U5Ds. We find that, in 2017, in the 100 LMICs, 26.4% of children 5 years of age were exposed to flood at least once during their life course, which was associated with 33,000 (95% confidence interval [CI] 4,000, 57,000) premature deaths. The chronic effect could be significantly larger than direct child mortality attributable to natural forces (i.e., 832 [95% CI 806, 856] U5Ds). The long-term health impacts of floods are nonnegligible, and the vulnerable communities identified in this study can help plan relevant climate-health services and public health interventions.