Prehistory of Native Americans of the Na-Dene language family remains controversial. Genetic continuity of Paleo-Eskimos (Saqqaq and Dorset cultures) and Na-Dene was proposed under the three-wave model of America's settlement; however, recent studies have produced conflicting results. Here, we performed reconstruction and dating of Na-Dene population history, using genome sequencing data and a coalescent method relying on rare alleles (Rarecoal). We also applied model-free approaches for analysis of rare allele and autosomal haplotype sharing. All methods detected Central and West Siberian ancestry exclusively in a fraction of modern day Na-Dene individuals, but not in other Native Americans. Our results are consistent with gene flow from Paleo-Eskimos into the First American ancestors of Na-Dene, and a later less extensive bidirectional admixture between Na-Dene and Neo-Eskimos. The dated gene flow from Siberia to Na-Dene is in agreement with the Dene-Yeniseian language macrofamily proposal and with the succession of archaeological cultures in Siberia.