This dataset includes the list of Stone Age settlement sites in the territory of Estonia. The list was compiled from published sources, grey literature and existing database records for unpublished sites. The current revision (version 1) of the dataset includes sites from recent systematic surveys conducted until 2017 (with some exceptional sites found later). Only sites with known exact locations were included into the dataset. The sites are classified into four stages of the Stone Age: pre-pottery Mesolithic (9000–5200 cal. BC), Narva (5200–3900 cal. BC), Comb Ware (3900–1800 cal. BC) and Corded Ware (2800–2000 cal. BC). The classification is based on typo-chronology of find materials, also using existing radiocarbon and other dating methods, if possible. The number of sites is 410, with 244 pre-pottery Mesolithic sites, 39 sites with Narva pottery, 60 sites with Comb Ware and 67 sites with Corded Ware. As there is a row dedicated to every habitation period in a location the number of unique site locations is smaller.