Shapiro was born in Jerusalem to Rabbi Avraham Shapira, the previous Rosh Yeshiva of Mercaz HaRav, and his wife, Penina Perl. He studied in the Yashlatz yeshiva high school, and then at Yeshivat Mercaz Harav. He was ordained by his father and Rabbi Shaul Yisraeli.
Rabbinic career
In 1983, his father appointed him as a lecturer in Mercaz Harav, and until 1993, he served as his father's right-hand man in the Chief Rabbinate. After his father's death in 2007, Rabbi Yaakov Shapira was appointed Rosh Yeshiva, in accordance with his father's will.