Rabbi Chizkiyah da Silva, called the Pri Chadash after his work, was born in Livorno, Italy, the son of Chacham David da Silva. Sources differ on the year: 5416 (1656) according to Hebrew sources, 1659 according to others. He began his studies under Chacham Shmuel Costa and Chacham Yehuda Sharaf.

At about twenty he moved to the Land of Israel and settled in Jerusalem, where he studied at the Beit Yaakov Vega yeshiva under the Rishon LeZion Rabbi Moshe Galante. He married Chana, daughter of the physician Rabbi Raphael Mordechai Malachi, and they had a son, Rabbi David. When Rabbi Moshe Galante died in 5449 (1689), he succeeded him as rosh yeshiva, before even reaching thirty.

When the yeshiva had to close for lack of funds, he went to Europe as an emissary between 1688 and 1692. In Amsterdam he was offered the post of rabbi of the Sephardic community, which he declined. There, in 5452 (1692), he printed the first part of his work, the Pri Chadash on the Shulchan Aruch, Yoreh De'ah. Back in Jerusalem he reopened his yeshiva with the support of the philanthropist Israel Jacob Pereira, hence its name Beit Yaakov Pereira, and headed it until his death. His students included Rabbi Yitzchak HaKohen Rapoport, author of Batei Kehunah, and Rabbi Shlomo Algazi, rabbi of Egypt.

The Pri Chadash examines earlier authorities in the light of the Talmud with great independence, not hesitating to dispute Rabbi Yosef Karo and the Rema. This freedom led the sages of Cairo to ban the book, a ban later lifted by Rabbi Avraham HaLevi, author of Ginat Veradim. The work went on to become a cornerstone of halachic ruling and is printed in most editions of the Shulchan Aruch; Rabbi Chaim ben Attar (the Ohr HaChaim) wrote Pri Toar to answer its objections. Works: Pri Chadash on Orach Chaim, Yoreh De'ah and Even HaEzer (the later parts published by his son), Mayim Chaim on the Talmud and Maimonides, and Binah VaDaat on bein hashmashot.

He passed away young, before the age of forty, on 28 Kislev 5456 (December 5, 1695) according to the tradition of his hillula; some sources place his death in 1698. He is buried on the Mount of Olives in Jerusalem, near the tomb of the prophet Zechariah.