BACKGROUND: Maternal mortality remains a tragedy and a key determinant for child survival. There is increasing evidence that the hazard ratio of demising for young children escalates after the death of their mothers, but few studies has been done in rural areas were HIV/AIDS is more prevalent. The aim of this study is to investigate the survival of children who lost their mothers soon or after their births in a rural setup with high HIV prevalence in South Africa. METHODS: This study used a data set from Africa Health Research Institute in rural South Africa.The study population comprised children (0-10 years of age) from 2000 to 2014. We employed a Cox regression modelling approach to estimate greatest temporal hazard of the child after the death of their mothers, accounting for the confounding influence of wealth index of the household and HIV status of the mother. RESULTS: We found 62,600 live births, and that 2191 children died when they were less than or equal to 10 years old. The mortality rates for < 5 and 5-9 years is 882.25 and 117.75 per 1000 live births respectively, with a maternal mortality rate of 447.3 deaths per 100,000 live births from 2000 to 2004. Child mortality risk was very high in less than 6 weeks after their mother's death (HR 3.45 [95%CI: 1.3-6.54]), and decreased drastically after 3 years following her death (HR 0.8 [0.2-6.3]). This increased risk was more pronounced among children aged less than 1 month and living in poor households. CONCLUSIONS: Children (less than 10 years) in rural households are at their highest risk of dying within 6 weeks of mother's death and this risk decreases substantially after the highly vulnerable window. This indicates that the period of mother's death does play a critical role on the survival of her children.Thus, understanding this risk and its timing in relation to a mother's death is critical to guide interventions and stress the relevance of assessing the interaction between clinical care and socio-economic programs in addressing the needs of orphans.