He was born in Syria in 1860, in the waning years of the Ottoman Empire. In his childhood, his family took refuge in Lebanon after their parish priest, St Joseph of Damascus (July 10) was martyred; but they later returned to Damascus. In 1879 he was tonsured a monk and entered into the service of Patriarch Hierotheos of Antioch. The Balamand Seminary had been closed since 1840, but the young monk was offered a scholarship at the Constantinople Patriarchate's seminary at Halki. Returning to Syria with a theological degree, St Raphael became assistant to Gerasimos, the new Patriarch of Antioch, traveling and preaching on his behalf. After further studies in Kiev, he transferred to the jurisdiction of the Patriarchate of Moscow and for a time was professer of Arabic studies at the Theological Academy in Kazan. (At that time the downtrodden Orthodox of the Middle East received considerable aid and theological training from the Tsar and from the Church in Russia).

In 1895 he was sent to the United States to shepherd the Arab Orthodox Community in New York, which was without a church or a priest. He quickly consecrated a chapel and with great energy set about the work of shepherding his flock there; but he was concerned not only for them but for the Arab Christian immigrants scattered through North America, most of whom were without a pastor and in danger of falling into heterodoxy or abandoning religious life. He traveled widely throughout the continent, visiting, counseling and serving Arab Christians, preaching, celebrating marriages and baptisms, receiving confessions and celebrating the Divine Liturgy, usually in private houses. In 1898 he published the first Orthodox prayer book in Arabic to appear in the New World. In 1899, he made a seven-month journey through forty-three American cities, seeking out the "scattered sheep" of the Church in America. His services were attended not only by Arabs but by Russians and Greeks, all of whom at that time depended on the Russian mission to North America. During this entire period, he held the official rank of Archimandrite, though his work and duties exceeded those of most bishops.

In 1901, Patriarch Meletios was elected to the see of Antioch, the first Arab to occupy the patriarchal throne for 168 years. Several proposals were made to elect Archimandrite Raphael to a see in Syria; but he refused all such offers, pointing out the Orthodox people's great and little-met needs in North America. In 1904, the Moscow Patriarchate made him Bishop of Brooklyn, the first Orthodox bishop to be consecrated on American soil. He redoubled his already impressive pastoral work, ordaining priests to the many new parishes that he had founded, and assisting Saint Tikhon (then Bishop of North America) in the care of his huge diocese. In 1905 he laid the foundation of the Monastery of St Tikhon in Pennsylvania.

The bishop saw the importance of integrating the faithful into the life of their new homeland, and was an early advocate of the use of English in American Church services. When Isabel Hapgood's Service Book — the first useful English translation of the Church's services — was published in 1906, he advocated its use in all his parishes.

In 1912, St Raphael was found to be suffering from heart disease, but continued his exhausting pastoral work for two more years. In 1915 he was finally unable to continue, and reposed after two months' illness.

When his relics were transported in 1998 from Brooklyn to Antiochian Village in Ligonier, PA, they were found to be incorrupt, and in 2000 he became the most recently glorified Saint of North America.

In North America St Raphael is commemorated on the anniversary of his repose: February 27 on the Civil/New Calendar, February 14 on the Julian Calendar. He is also commemorated with the Synaxis of Saints of North America on the Second Sunday after Pentecost. The Patriarchate of Antioch also commemorates him, but on Saturday before the Synaxis of the Archangels (November 8).