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Households are where children are born and grow up, where they receive essential care, including time, socio-psychological support and economic resources. Households can also change over a child’s life. We consider the dynamic role of household structure in child mortality in South and Eastern Africa using longitudinal data from 16 Health and Demographic Surveillance Systems between 1990 and 2016, covering ~625,000 under-five year olds. We account for household structure as time-varying, using the number of household members by age and sex, and a typology of households, in semi-parametric Cox models estimating the risk of death among under-five year olds. We find that under-five year old children experience on average six changes in household structure. In contrast to expectations, more working aged adults in the household does not reduce the risk of child death. The presence of over 65 year olds in the household adversely affects child survival, likely because they are also dependents, competing for resources. Our findings suggest that (in)stability of households is important to consider in evaluating child survival.