Improved resolution data from radiocarbon, climate and ancient DNA studies of megafauna and humans is providing the first ability to disentangle the roles of climate change and human impact in the Late Pleistocene megafaunal extinctions. We find that megafaunal populations underwent repeated local or global extinctions in association with rapid warming events on a millennial scale. The extinction events took place both before and after the presence of modern humans on the landscape. Human impacts may be through the disruption of metapopulation processes which appear to stabilise ecosystems, and may have evolved to provide resilience to rapid and frequent climate shifts in the past. Globally, we see a strong correlation between warming events at the end of the last Glacial and isotopic signatures in megafaunal bones characteristic of rapid increases in environmental moisture levels. It appears that moisture-caused fragmentation of grasslands was a key driver of the Late Glacial megafaunal extinctions, and that the constant presence of grasslands in Africa explains the relative lack of extinctions during this time. In the Americas, the rapid movement of the first Native Americans throughout both continents creates a powerful and unique model system due to the opposing climate trends in each hemisphere at the time. While megafaunal extinctions were associated with warming trends in both cases, the out of phase climate patterns caused the sequence and timing of events to be mirrored, providing a unique high resolution view of the interactions of human colonisation and rapid climate change on megafaunal ecosystems.