Burial assemblages inform us about the biology of past societies, social relations, and ritual and symbolic behavior. However, they also allow us to examine the circumstances of death and social violence. A high level of intergroup violence among prehistoric hunter-gatherers is well-documented in some times and places but is extremely rare in others. Here we present an analysis of the perimortem injury to skeleton PD8 at the site of Sphinx in Central Sudan. This burial, attributed to the Early Khartoum (Khartoum Mesolithic) culture, radiocarbon dated between 8637 and 8463 cal BP, bears evidence of a perimortem sharp force trauma caused by penetration of an unshaped, fractured non-human bone between the right scapula and the rib cage. Among more than 200 anthropologically assessed human burials from the early Holocene Nile Valley reviewed in this paper, PD8 provides the only documented evidence of violence resulting in death. This rare case of death differs from the numerous cases of intergroup conflict documented in terminal Pleistocene burial grounds in Lower Nubia. This suggests different patterns of violence and strategies of conflict resolution in the pre-Neolithic (terminal Pleistocene and early Holocene) Nile Valley. We attribute this difference in the prevalence of interpersonal trauma to climatic and environmental conditions, territorial boundary defense, and post-marital residence practices before and after the Younger Dryas’ arid millennium (~ 12,800–11,600 BP).