Efraim Yaakov was born in 1953 and raised in Nahariya, to a family from Hogeriya in Yemen. He completed his academic degrees in the Department of History and Philosophy at the Hebrew University, where he served as an assistant to Prof. Yeshayahu Leibowitz. He wrote the M.A. and his doctoral dissertations on Kabbalah among Yemeni Jews under the supervision of Prof. Moshe Idel. In addition to his academic studies, he studied halakha with two of the greatest rabbis of Yemeni Jewry in Israel: Mary Yosef Kapach and Mary Chaim Yahya Sinwani.