Hasekura Tsunenaga was born in year 2 of the Genki era (1571) in Ushū, Okitama-no-kōri, Nagai-sō, Tateishi-mura (now part of modern day Yonezawa in Yamagata Prefecture. He was the son of (), who had ancestral ties with Emperor Kanmu. He was a mid-level noble samurai in the Sendai Domain in northern Japan who had the opportunity to directly serve the daimyō, Date Masamune, and received an annual stipend of 1200 koku. He spent his young adulthood at Kamitate Castle () that was constructed by his grandfather Hasekura Tsunemasa (). The place of origin of the family name "Hasekura" was Hasekura Village (), now Hasekura Ward () in Kawasaki City.