After his entrance into the Jesuit order, he taught for several years at Georgetown, and became the pastor of St. Joseph's Church in Baltimore, where he took uncommon measures to integrate black Catholics and Italian immigrants into parish life.

On his mother's side, his ancestry included some of the early settlers of Maryland, North Carolina, and Kentucky.

[2] When the Society of Jesus was suppressed worldwide, the Jesuit president of Gonzaga, Jeremiah Keily, disobeyed his superiors by attempting to continue the operation of the school.

[2] Clarke entered the Society of Jesus on August 14, 1833, and was sent to the Jesuit novitiates at White Marsh Manor, and then Frederick, Maryland.

[5] His health rapidly failed in 1846 and, fearing for his life, his superiors sent him to Bohemia Manor, Maryland, to recuperate.

[5] Succeeding John Early,[6] he remained for only two years, before being appointed president of Gonzaga College in Washington, D.C.,[7] to replace Charles H.

[6] He also succeeded John Early as pastor of St. Ignatius Church in the city in October 1858,[10] and held the post until he was replaced by O'Callaghan the following year.

This parochial school was moved to a property owned by Senator Stephen Douglas that he rented on I Street on September 24, 1860.

In his later years, he remained an active preacher, delivering sermons to mark major occasions and anniversaries in Baltimore, Washington, and Philadelphia.

[15] He came to be considered an authority who was consulted on theological questions, and he catechized students, resulting in a substantial number of conversions to Catholicism.