James Margetson (1600 – 26 August 1678) was an English churchman, Church of Ireland Archbishop of Armagh from 1663.
He was a native of Drighlington in Yorkshire. He was educated at Peterhouse, Cambridge, and returned after ordination to Yorkshire, where he attracted the notice of Thomas Wentworth, then Lord President of the North, who took him as chaplain to Ireland in 1633. He was made dean of Waterford by patent, 25 May 1635, and in October was presented by the crown to the rectory of Armagh, Cavan. He resigned Waterford and Armagh in 1637, and in that year became rector of Galloon in Monaghan and dean of Derry. In December 1639 Margetson was made dean of Christ Church Cathedral, Dublin. No new dean of Derry was appointed until after the Restoration. It appears from the correspondence of William Laud and Strafford (as Wentworth now was) intended to restore the almost ruinous cathedral of Christ Church, but that he found neither time nor money. Margetson was prolocutor of the lower house of convocation in 1639.
When the Irish Rebellion of 1641 broke out, Margetson was distressed from the failure of income; by 1647 Dublin was in the hands of the English parliament, and the Anglican clergy were invited to use the Directory of Public Worship instead of the Book of Common Prayer; ane bishop and seventeen clergymen, of whom Margetson was one, refused to hold their churches on these terms. Ormonde left Ireland 28 August 1647, and Margetson fled to England about the same time. He suffered imprisonment at Manchester and elsewhere, but was afterwards allowed to live in London unmolested, but very poor. He was employed by royalists to dispense money among distressed supporters, in England and Wales, and William Chappell may have been one who was supported in this way.