We measured 87Sr/86Sr for all available human remains (n = 40) dating from the Mesolithic to the Bronze Age (ca. 6400–800 cal BC) in Lithuania. In addition, local baselines of archaeological fauna from the same area were constructed. We identified significant and systematic offsets between 87Sr/86Sr values of modern soils and animals and archaeological animals due to currently unknown reasons. By comparing 87Sr/86Sr human intra-tooth variation with the local baselines, we identified 13 non-local individuals, accounting for 25–50% of the analysed population. We found no differences in the frequency of local vs. nonlocals between male and female hunter-gatherers. Six Mesolithic-Subneolithic individuals with 87Sr/86Sr values > 0.7200 may have come from southern Finland and/or Karelia. Two Mesolithic-Subneolithic individuals from the Donkalnis cemetery with 87Sr/86Sr values < 0.7120 likely came from the Lithuanian Baltic coast. These data demonstrate coastal-inland mobility of up to 85 km, which is also supported by archaeological evidence. The standard deviation in the intra-tooth 87Sr/86Sr indicates that mobility did not decrease with the adoption of pottery technology at ca. 5000 cal BC but rather slowly decreased during the Neolithic and Bronze Age periods. We interpret this as a result of the introduction and subsequent intensification of farming. The least mobile way of life was practised by Subneolithic coastal communities during the 4th millennium cal BC, although 87Sr/86Sr do not exclude that they migrated along the coastline.