Variations in human subsistence and settlement patterns have been documented at Holocene archaeological sites across Island and Mainland Southeast Asia. Although climate is frequently invoked as a causal mechanism underlying this variation, direct evidence of ancient rainfall variability on the scale of human lifetimes has thus far been elusive. Here we use a novel time-resolute method for in situ measurement of human tooth enamel δ18O values (n = 2629 near-weekly measurements sampling 51 years) to assess past rainfall seasonality patterns in Southeast Asia. Seasonal fluctuations in enamel δ18O values of ancient humans from several different periods are compared to modern rainfall recorded in Vietnam, Philippines, and Indonesia by the Global Network in Isotopes in Precipitation (GNIP). The likelihood that the ancient humans reflect local precipitation patterns is established through measurement of bulk enamel 87Sr/86Sr ratios. Comparison of the archaeological individuals and the modern rainfall datasets shows that the seasonal variabilities in ancient δ18Oenamel are consistent with seasonal variabilities in modern δ18Oprecip across the study locations (highest in Vietnam, lowest in Indonesia, intermediate in the Philippines). Strong seasonal δ18Oenamel trends in four of five hunter-gatherers from Con Co Ngua, Vietnam, facilitate the inference of birth approximately six months prior to the onset of monsoons, consistent with tropical subsistence societies where food availability correlates with rainfall. High-resolution analysis of human tooth enamel represents a powerful new tool for seasonality reconstructions across different regional and climatic settings.