- A Letter to the Roman Catholics of the City of Worcester, From the Late Chaplain of That Society. Stating the Motives Which Induced him to Relinquish ... and Become a Member of the Protestant Church
- A Sermon on the Relations of the Christian Ministry: Preached at St. Peter's and Christ Church, in the City of Philadelphia, the Second Day of October, 1785.
- A reply to An address to the Roman Catholics of the United States of America. By the author of A letter to the Roman Catholics of the city of Worcester.
- The Remains of the REV. Charles Wharton, D.D.: With a Memoir of His Life Volume 1
- The Remains of the Rev. Charles Wharton, D.D. with a Memoir of His Life