In 1858 The rectorate was assumed by the Rev. Dr. Joseph Morrison Clarke, who had grown up in Skaneateles, NY. He was ordained in 1852 and while serving as the pastor of St. Peter’s Church in Niagara Falls came to know Dr. Gregory, who recommended him for the upcoming vacancy at St. James. When Bishop Huntington started the second hospital in Syracuse — the House of the Good Sheppard — in 1872, Dr. Clarke also served as one of its chaplains.
Dr. Clarke ministered not only to his parish, but made himself available to anyone in the community who was in need of a clergyman. He was highly respected, but in 1866 was publicly criticized in the Courier newspaper by a Roman Catholic priest named Father Moriarty, who accused him of marrying “Negroes, Jews, Irish and Germans” - and hinted darkly that he should stick to marrying only those of his own flock. In a letter published in the Courier of April 27, 1886 Dr. Clarke replied:
“Am I to understand that Father Moriarity refuses to marry Negroes, Irish, Germans, etc. or is it only that such persons of those different nationalities as cannot afford to pay his fees come to me instead? I have married Negroes, Indian couples and other nationalities he speaks of. I am not at all ashamed of being the minister of the poor,nor do I think it unfitting that when people generally indifferent to religion, yet desire the priest’s services at funerals, at infant baptisms, and at marriages, he should take the opportunity to introduce as much religion as he can into their lives. Most of Father Moriarity’s reasoning in reply to my lecture rests upon that confusion between “Roman” and “Catholic” which is the main stock in trade for his side of the controversy.”
Dr. Clarke left St. James on October 1, 1886 — the 28th anniversary of his arrival — to accept the professorship of Hebrew and exegesis at the Episcopal Theological Seminary in Nashotah, Wisconsin.
Following his retirement in 1891, he returned to Syracuse and became chaplain to Bishop Huntington, a post he held for the remainder of his life.
He delivered major addresses at both the cornerstone laying of the new St. James Church and at its opening. Thereafter, he was a regular attendant and frequent speaker among his old congregation. He lived to see it revived as the Church of the Saviour and when he died on November 30, 1899 his body lay there in state.