The drivers of the global Quaternary megafaunal extinction are constantly being updated and discussed. Most paleoarchaeological sites in South America with proboscideans and humans in association are considered as clear killing sites, an interpretation that might not consider their taphonomic aspects and neglect other ecological interactions. Here we describe a unique example of megafaunal killing by humans in South American, a skull of a young Notiomastodon platensis from Brazil with an artifact embedded in its rostral area. This fossil proboscidean is from Lagoa Santa Karst, the homeland of some of the oldest evidence for humans in South America, the Lagoa Santa culture. The late Pleistocene/early Holocene deposits from Lagoa Santa may record a bottleneck ecological process for megafaunal populations, and the hunting activity of past humans perhaps played an important role in Notiomastodon platensis extinction.