After a short period at Pembroke College, Cambridge in the early 1660s, he moved on in Lent term 1660 to New Inn Hall, Oxford, and graduating B.A.
[1][2] In 1684 Wagstaffe was preferred to the chancellorship of Lichfield Cathedral and a prebend, by James II, Bishop Thomas Wood being incapacitated through suspension.
In the same year, also at the presentation of the king as patron of the rectory of St. Gabriel Fenchurch, London (with St. Margaret Pattens); he was deprived at the Glorious Revolution of both posts, since he refused to take the new oaths.
For some time he made his living by practising as a physician, still wearing clerical dress, and treating William Sancroft and Francis Turner, Bishop of Ely.
Mr. Giffard at Southgate in the parish of Enfield, near London, which apparently was occupied by White, the deprived bishop of Peterborough.
[1] Wagstaffe passed much of the rest of his days in Warwickshire, but was present when holy communion was given to John Kettlewell on his deathbed in London in 1695.
[1] The Post Boy of 23–5 October 1712 recorded his death: "On Friday the 17th instant died the Reverend Dr. Wagstaffe, at his house at Binley, near Coventry.
He was a person of extraordinary judgment, exemplary piety, and unusual learning; and had he not had the misfortune to dissent from the established government by not taking the oaths, as he had all the qualities of a great divine, and a governor of the church, so he would have filled deservedly some of the highest stations in it.
[1] The authorship of Eikon Basilike, a work of royalist apologetics published in 1649 shortly after the execution of Charles I, flared up as a topic of controversy in the 1690s.
[4][5] A few years later, Wagstaffe returned to the table-turning attack on Milton's integrity, in replying to the Amyntor of John Toland.
[6] Wagstaffe gave an account of Archbishop Sancroft's illness and death, in A Letter out of Suffolk (1694; reprinted in Somers's Tracts, 1751).
Wagstaffe contrasted the severity with which the nonjurors were treated with the comparative leniency of Cromwell under the Commonwealth, or Elizabeth, towards Catholics.