Charles Henry Wharton (5 June, 1748 in St. Mary's County, Maryland – 22 July, 1833 in Burlington, New Jersey) was a clergyman.

The family plantation, Notley Hall, was presented to his grandfather by Lord Baltimore. In 1760 he was sent to the English Jesuit College at St Omer, where he was very studious, and acquired the Latin tongue with such proficiency as to converse in it.

He was ordered deacon in June, 1772, and priest the following September, both in the Roman Catholic Church. At the close of the American Revolution he 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).

He returned to what had become the United States in 1783 in the first vessel that sailed after the peace. In May, 1784, having adopted the views of the Church of England, he published his celebrated "Letter to the Roman Catholics of Worcester" (Philadelphia, 1784), and became rector of Immanuel Church, New Castle, Delaware. At the general convention of 1785 he was on the committee to "draft an ecclesiastical constitution for the Protestant Episcopal church in the United States", also on the committee "to prepare a form of prayer and thanksgiving for the Fourth of July", and that to Americanize the Book of Common Prayer. In 1786 he was elected a mere-bet of the American philosophical society.

After ten years' further residence in Delaware, he became, in 1798, rector of St. Mary's Church, Burlington, New Jersey. In 1801 he accepted the presidency of Columbia College, New York, and was to assume the position at the August commencement ceremonies, but he did not appear for them, and resigned in the fall. He returned to his rectorship in Burlington, which he held till his death in 1833.

He was always president of the standing committee of the diocese and a deputy to the general convention, and among the first in scholarship and influence of the clergy of his church in the United States. The testimony of his contemporaries and his numerous publications pronounced him an accomplished divine, a gifted poet, and an able controversialist. At the time of his decease he was the senior presbyter of the Protestant Episcopal Church. Besides the works already mentioned, he published "Reply to an Address [by Bishop Carroll] to the Roman Catholics of the United States" (Philadelphia, 1785); "Inquiry into the Proofs of the Divinity of Christ" (1796); and "Concise View of the Principal Points of Controversy between the Protestant and Roman Churches" (New York, 1817). In 1813-14 he was co-editor, with Reverend Dr. Abercrombie, of the Quarterly Theological Magazine and Religious Repository. His "Remains," with a memoir, were published by Bishop George W. Doane (2 vols., Philadelphia, 1834).

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