Background The effect of the period before a mother’s death on child survival has been assessed in only a few studies. We conducted a comparative investigation of the effect of the timing of a mother’s death on child survival up to age five years in rural South Africa. Methods We used discrete time survival analysis on data from two HIV-endemic population surveillance sites (2000–2015) to estimate a child’s risk of dying before and after their mother’s death. We tested if this relationship varied between sites and by availability of antiretroviral therapy (ART). We assessed if related adults in the household altered the effect of a mother’s death on child survival. Findings 3,618 children died from 2000–2015. The probability of a child dying began to increase in the 7–11 months prior to the mother’s death and increased markedly in the 3 months before (2000–2003 relative risk = 22.2, 95% CI = 14.2–34.6) and 3 months following her death (2000–2003 RR = 20.1; CI = 10.3–39.4). This increased risk pattern was evident at both sites. The pattern attenuated with ART availability but remained even with availability at both sites. The father and maternal grandmother in the household lowered children’s mortality risk independent of the association between timing of mother and child mortality. Conclusions The persistence of elevated mortality risk both before and after the mother’s death for children of different ages suggests that absence of maternal care and abrupt breastfeeding cessation might be crucial risk factors. Formative research is needed to understand the circumstances for children when a mother is very ill or dies, and behavioral and other risk factors that increase both the mother and child’s risk of dying. Identifying families when a mother is very ill and implementing training and support strategies for other members of the household are urgently needed to reduce preventable child mortality.