An observational sibling case-control study examined the effect of exposure to cyclones in the past 3 months on under-5 mortality in 34 low- and middle-income countries. The study included 100,798 child deaths and 247,445 controls from 1993 to 2021. After adjustment for meteorological, temporal factors and maternal age, a significant association was found with exposure in the past 3 months (OR: 1.030, 95% CI: 1.002, 1.075; p = 0.041). The strongest effect was in the first month before death (OR: 1.101, 95% CI: 1.039, 1.166; p < 0.001), with attenuation in the second and third months. Exposure 0 to 30 days before death is estimated to have caused 0.85 million deaths (95% CI: 0.35 million, 1.32 million) in cyclone-exposed countries in 2000–2020. The study highlights possible limitations such as misclassification of exposure from dichotomous classification and self-report data. The conclusion emphasizes the need for strategies to increase resilience, such as improving access to water and sanitation.