At the close of the American Revolution Wharton resided at Worcester, England, as chaplain to the Roman Catholics in that city.

There he addressed a poetical epistle to George Washington, with a sketch of his life, which was published for the benefit of American prisoners in England (Annapolis, 1779; London, 1780).

After ten years' further residence in Delaware, in 1798 Wharton accepted a position as rector of St. Mary's Church, Burlington, New Jersey, where he would serve the rest of his life.

Wharton served as president of the standing committee of the diocese of New Jersey, and several times as a deputy to the General Convention.

Wharton accepted the presidency of Columbia College, New York, conditioned upon his ability to also continue his position in Burlington.