Hacham Shem Tob Gaguine was born to Rivka and Hacham Yitzhak on the 15th of Elul, 5645 (1885) in Jerusalem.
His grandfather's grandfather was kabbalist Hacham Sar Shalom Sharabi, and his great-grandfather was Hacham Haim Avraham Gaguine, who was the first person to be appointed to the Hacham Bashi (Chief Rabbi) position in the Land of Israel, a position which was later to known as the Rishon LeZion. Hacham Shem Tob Gaguine attended the Doresh Zion School and later studied with kabbalist Hacham Yaakov Alfiayah. In 1908 he received certification as a teacher from Rabbi Haim Berlin.
In 1913 he moved to Cairo where he served as a member of the Beit Din for both the Sephardi and Ashkenazi communities. In 1920, he moved to England where he served as rabbi of a Sephardi community and was a member of the Beit Din for the Ashkenazi communities in Manchester.
In 1921 he relocated to London to officiate as Rosh Beit Din for the Sephardi communities. In 1929 he was appointed Rosh Yeshiva at Ohel Moshe VeYehudit, named after the Montefiore couple, in the city of Ramsgate. In 1933 he was elected Vice-Chairman of the Rabbinical Committee of England and officiated as Rosh Yeshiva of Etz Hayim in London.
Hacham Shem Tob Gaguine passed away on the 18th of Av, 5713 (1953).
Among his publications are the Keter Shem Tob, on Sephardi and Ashkenazi customs, and Jewish Life in Cochin, on the Jewish community of Cochin. He wrote for Jewish newspapers in England, such as the Israel Messenger and the Jewish Chronicle, as well as for Hebrew journals such as HaHavatzellet, and for the Hame'aseph collection of Torah innovations. Additional Torah innovations of his were published in books by Hacham Moshe Elyashar and Hacham Aharon Elhadif, and a book of his poems has also been published. Several works of commentaries by Hacham Shem Tob Gaguine still remain in manuscript form.