Saphir was born in Ashmyany in the Russian Empire (now Belarus) and immigrated to Ottoman Palestine as a child with his family in 1832. His parents, who were from the Perushim community, settled in Safed. Within a year his father died and a month later his mother died. At the age of 12, he witnessed the attack by the Arabs of the Galilee on the Jews of Safed in the lunar month of Sivan, 1834. He moved to Jerusalem in 1836.
In 1848, he was commissioned by the Jewish community of the latter city to travel through the southern countries to collect alms for the poor of Jerusalem. In 1854 he undertook a second tour to collect funds for the construction of the Hurva Synagogue in the Jewish Quarter, which led him in 1859 to Yemen, British India, Egypt, and Australia.
The result of this journey was his momentous ethnographic work, entitled `Even Sapir,[1] a travel diary and vignette of Jewish life and history in Yemen. Saphir published also Iggeret Teman (Wilna, 1868, consciously titled after Rambam's letter of centuries earlier), a work on the appearance in Yemen of the pseudo-MessiahJudah ben Shalom, and which was largely responsible for ending Judah ben Shalom's career. Saphir died in Jerusalem in 1886.
Saphir was the first Jewish researcher to recognize the significance of the Cairo geniza, as well as the first to publicize the existence of the Midrash ha-Gadol, both later studied with great panache by Solomon Schechter.
In the years 1833–1885, Saphir helped print the book Ḥemdat Yamim (reprinted Jerusalem 1977) by the arch-poet of Yemen, R. Shalom Shabazi, and even added an introduction to it.
^Hirschfeld, Hartwig; Montefiore Library. Jews' College. (1904). Descriptive catalogue of the Hebrew MSS. of the Montefiore Library. London:Macmillan. p. 121. Internet Archive website Retrieved 24 April 2018.