Horse sacrifice and deposition are enigmatic features of funerary rituals identified across prehistoric Europe that persisted in the eastern Baltic. Genetic and isotopic analysis of horses in Balt cemeteries [1st to 13th centuries CE (Common Era)] dismantle prevailing narratives that locally procured stallions were exclusively selected. Strontium isotope analysis provides direct evidence for long-distance (~300 to 1500 kilometers) maritime transport of Fennoscandian horses to the eastern Baltic in the Late Viking Age (11th to 13th centuries CE). Genetic analysis proves that horses of both sexes were sacrificed with 34% identified as mares. Results transform the understanding of selection criteria, disprove sex-based selection, and elevate prestige value as a more crucial factor. These findings also provide evidence that the continued interaction between pagans and their newly Christianized neighbors sustained the performance of funerary horse sacrifice until the medieval transition. We also present a reference 87Sr/86Sr isoscape for the southeastern Baltic, releasing the potential of future mobility studies in the region.