Climate change is reshaping the Earth's hydrological cycle. Such changes impact children's health through multiple pathways. Here we show that, in 59 low- and middle-income countries, although sufficient annual rainfall decreases under-five child mortality, anomalies in seasonal rainfall could increase under-five mortality. The risk associated with rainfall scarcity (odds ratio 1.15, 95% confidence interval (CI) 1.11-1.20) was much higher than that associated with rainfall surplus (odds ratio 1.04, 95% CI 1.02-1.06). Extreme rainfall amounts and the number of wet days are positively associated with elevated under-five child mortality. These risks were more pronounced for children from rural areas, families with lower educational attainment and households that depend on natural water sources. From 2000 to 2020, rainfall variations, extreme daily rainfall events and the number of wet days are estimated to cause 290 under-five child deaths per 10,000 persons annually (95% CI 177- 417). This investigation provides important insights into the overlooked health consequences of rainfall pattern changes on vulnerable populations.