Background Climate change has exacerbated the frequency, intensity, and impacts of extreme weather events (EWEs), such as tropical cyclones. However, the increasing impact of tropical cyclones on child mortality, especially in low- and middle-income countries (LMICs), remains understudied. Methods and findings Utilizing individual-level data from the Demographic and Health Surveys, we conducted a sibling-matched case-control study to assess the impact of cyclone exposure over the past 3 months on under-five mortality. The study included 100,798 under-five deaths and 247,445 controls across 34 LMICs from 1993 to 2021. After adjusting for key meteorological and temporal confounders and maternal age, significant positive associations were observed between under-five deaths and cyclone exposure over the past 3 months before death (odds ratio [OR]: 1.038, 95% confidence interval [CI]: 1.002, 1.075; p = 0.041). Specifically, the strongest effects were observed in the first month before death (OR: 1.101, 95% CI: 1.039, 1.166; p < 0.001), diminishing in the second and third months before death. We estimated that cyclone exposure 0–30 days before death may have caused 0.85 million under-five deaths (95% CI: 0.35 million, 1.32 million) in countries exposed to cyclones from 2000 to 2020. As an observational study, its use of self-reported data and dichotomous exposure assessment may introduce recall bias and exposure misclassification, limiting accuracy and representativeness. Conclusions This global analysis demonstrates the substantial under-five mortality risk from cyclones, emphasizing the importance of targeted strategies to enhance community resilience against the growing threat of EWEs on children, such as improving access to water sources and sanitation facilities.