Hacham Raphael Aaron Ben Shimon was born in 1848 to Rachel and Hacham David Ben Shimon, author of the Tzuf Devash, in Rabat, Morocco. In 1854, at the age of six, he immigrated to the Land of Israel with his family. Hacham Raphael Aaron Ben Shimon served as secretary of his father's rabbinic court, and became Head of the Magen David Yeshiva in Jerusalem.
In 1860, he married Esther Ben Oualid. In 1888, he was sent back to Morocco by the Va'ad Ha'Eda HaMa'aravit (Maghreb Community Committee) as a rabbinic emissary. While staying in the city of Fes, Hacham Raphael Aaron Ben Shimon founded the Dovev Sephat Yesheinim committee, whose objective was to collect the manuscripts of Morocco's sages and have them published.
In 1891, after returning from Morocco, he was appointed Chief Rabbi of the Cairo Jewish community, a role he was to fill for three decades (1891 – 1921). During his term, he was decorated with honorary awards by the Ottoman and Egyptian governments.
During the First World War, he combatted anti-Semitic incitement in El Aqdam, an Egyptian newspaper. Hacham Raphael Aaron Ben Shimon wrote the newspaper's owners – Princess Alexandra – a letter. In her reply to the sage she wrote, "Thank you for alerting us to the errors and crimes issued by the newspaper […] against the nation that I respect and laud", and dismissed the newspaper's editor.
In 1921, he immigrated to the Land of Israel with his family, settling in Tel Aviv–Yaffo. He maintained a synagogue in his home in Tel Aviv, and the chief rabbis of Tel Aviv–Yaffo would consult him on legal and Halakhic matters.
Hacham Raphael Aaron Ben Shimon passed away in Tel Aviv on 10 Heshvan 5689 (24 October, 1928) and was buried on the Mount of Olives in Jerusalem. Some two months later, his wife passed away and was buried alongside him.
Hacham Raphael Aaron Ben Shimon had the merit of writing valuable books and having had them published during his lifetime. Among his works are Nehar Pakod – complements to his father's book, Sha'ar HaMefaked – on the customs in Jerusalem; Nehar Mitzraim, in two parts – on customs and laws in Egypt, written in the order of the Shulchan Aruch; Seder Halitza – on the laws of halitza [the Jewish ritual whereby a widow is freed from the biblical obligation of marrying her brother-in-law (levirate marriage) in cases where her husband died without issue]; Tuv Mitzraim – on the sages and ge'onim of Egypt from Maimonides' time on; Umtzor Devash – Responsa; Lehem HaMa'arechet in three parts – sermons; Bat N'aot Hameradot – on laws concerning a dissenting spouse.