Henry Wilkinson (1616–1690) was an English clergyman and academic, Principal of Magdalen Hall, Oxford and White's Professor of Moral Philosophy, and later an ejected minister.
He was the son of William Wilkinson, curate or chaplain of Adwick-le-Street, Yorkshire and born there. John Wilkinson, Principal of Magdalen Hall and President of Magdalen College, Oxford, is stated by Anthony Wood to have been his uncle.
After some time at Edward Sylvester's school, Oxford, Henry matriculated from Magdalen Hall on 10 October 1634, aged 17. He graduated B.A. on 28 November 1635, M.A. on 26 May 1638, and became a noted tutor and dean of his house. When the First English Civil War broke out, Wilkinson left Oxford and joined the parliament, took the Solemn League and Covenant, and became a preacher in much request. He was appointed lecturer or minister of Buckminster, Leicestershire, in 1642, and was instituted vicar of Epping, Essex, on 30 October 1643.
He was appointed one of the parliamentary visitors of Oxford University on 1 May 1647. He was created B.D. on 14 April 1648, fellow and vice-president of Magdalen College on 25 May, principal of Magdalen Hall on 12 August 1648, and White's Professor of Moral Philosophy on 24 March 1649. A strong parliamentarian, Wilkinson entertained Oliver Cromwell, Thomas Fairfax, and the other commanders at Magdalen Hall on 19 May 1649, and, preaching before them next day, ‘prayed hard for the army’. A salary for preaching regularly at Carfax was voted him by the council of state on 27 May 1658.