BACKGROUND: Half of under-5 deaths in South Africa occur at home, however the reasons remain poorly described and data on the care pathways during fatal childhood illness is limited. This study aimed to better describe care-seeking behavior in fatal childhood illness and to assess barriers to healthcare and modifiable factors that contribute to under-5 deaths in rural South Africa. METHODS: We conducted a social autopsy study on all under-5 deaths in two rural South African health and demographic surveillance system sites. Descriptive analyses based on the Pathways to Survival Framework were used to characterise how caregivers move through the stages of seeking and providing care for children during their final illness and to identify modifiable factors that contributed to death. FINDINGS: Of 53 deaths, 40% occurred outside health facilities. Rates of antenatal and perinatal preventative care-seeking were high: over 70% of mothers had tested for HIV, 93% received professional assistance during delivery and 79% of children were reportedly immunised appropriately for age. Of the 48 deaths tracked through the stages of the Pathways to Survival Framework, 10% died suddenly without any care, 23% received home care of whom 80% had signs of severe or possibly severe illness, and 85% sought or attempted to seek formal care outside the home. Although half of all children left the first facility alive, only 27% were referred for further care. CONCLUSIONS: Modifiable factors for preventing deaths during a child's final illness occur both inside and outside the home. The most important modifiable factors occurring inside the home relate to caregivers' recognition of illness and appreciation of urgency in response to the severity of the child's symptoms and signs. Outside the home, modifiable factors relate to inadequate referral and follow-up by health professionals. Further research should focus on identifying and overcoming barriers to referral.