Bogoraz was born in the city of Ovruch in the family of a Jewish school teacher. Bogoraz changed his birthname from Natan to Vladimir after he converted to Christianity in adulthood. After finishing Chekhov Gymnasium in 1882, he enrolled in the Faculty of Law of Saint Petersburg University, but was dismissed for revolutionary activity with Narodnaya Volya and exiled to his parents' home in Taganrog. He spent 11 months at Taganrog prison for revolutionary propaganda. In 1886, he moved to Saint Petersburg, where he was arrested and later exiled into northeastern Siberia, near Yakutsk (1889–1899), where he studied the Chukchi people, their way of life, traditions, language, and beliefs, giving him valuable material for poems and belletristic essays. Allegedly, Bogoraz attained fluency in the Chukchi language and partial fluency in the Even language.
