He was the second son of Henry Wharton of Wharton and Agnes Warcop, and younger brother of Thomas Wharton, 1st Baron Wharton. He was educated at Trinity College, Oxford, where he graduated M.A., 3 February, 1564, and afterwards became a Fellow.
In 1583 he entered the English College at Reims to study for the priesthood (28 July). He was ordained priest in the following year 31 March, but continued his studies after ordination till 1586, when on 21 May he left Reims in company with Edward Burden.
No details of his missionary work have been preserved; but at his trial Baron Savile, the judge, incidentally remarked that he had known him at Oxford some years after 1596. He was finally arrested in 1599 at the house of Eleanor Hunt, a widow, who was arrested with him and confined in York Castle. There, with other Catholic prisoners, he was forcibly taken to hear Protestant sermons.
He was brought to trial together with Mrs. Hunt at the Lent Assizes 1600, and both were condemned, the former for high treason, the latter for felony. Both refused life and liberty at the price of conformity. Eleanor Hunt died in prison.
- Thomas Worthington, A Relation of Sixteen Martyrs (Douai, 1601);
- Douay Diaries (London, 1878);
- Richard Challoner, Memoirs of Missionary Priests (London,1741-42);
- John Morris, Troubles of our Catholic Forefathers, III (London), 462