Recent advances in the use of summed probability distribution (SPD) of calibrated C dates have opened new possibilities for studying prehistoric demography. The degree of correlation between climate change and population dynamics can now be accurately quantified, and divergences in the demographic history of distinct geographic areas can be statistically assessed. Here we contribute to this research agenda by reconstructing the prehistoric population change of Jomon hunter-gatherers between 7,000 and 3,000 cal BP. We collected 1,433 C dates from three different regions in Eastern Japan (Kanto, Aomori and Hokkaido) and established that the observed fluctuations in the SPDs were statistically significant. We also introduced a new non-parametric permutation test for comparing multiple sets of SPDs that highlights point of divergences in the population history of different geographic regions. Our analyses indicate a general rise-and-fall pattern shared by the three regions but also some key regional differences during the 6th millennium cal BP. The results confirm some of the patterns suggested by previous archaeological studies based on house and site counts but offer statistical significance and an absolute chronological framework that will enable future studies aiming to establish potential correlation with climatic changes. ; EC and MM were funded by a Marie-Curie Intra-European Fellowship (grant #625863, url: http://cordis.europa.eu/mariecurie-actions/eif/home.html). SimulPast Project (Consolider-Ingenio CSD2010-00034) also provided funding and it was conducted in collaboration with the “Long-term Sustainability through Place-Based, Small-Scale Economies: Approaches from Historical Ecology” Project (R-09) at the Research Institute for Humanity and Nature, Kyoto, Japan. ; Peer Reviewed