Thomas Wagstaffe the Elder (13 February, 1645 – 17 October, 1712) was a clergyman of the Church of England, after the nonjuring schism a bishop of the breakaway church.
Wagstaffe was born on 13 February 1645 at Binley in Warwickshire, and was named after his father, who had settled there and married Anne Avery of Itchington; he was related to Sir Joseph Wagstaffe and to William Wagstaffe the physician. He was educated at Charterhouse School. 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. on 15 October 1664, M.A. on 20 June 1667. Two years later he was ordained deacon by John Hacket, Bishop of Lichfield, and in the same year priest by Joseph Henshaw, Bishop of Peterborough, on his institution to the benefice of Martinsthorpe. He became chaplain to Sir Richard Temple, 3rd Baronet (1634–1697), and was made curate of Stowe.
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. With Archbishop Sancroft he spent some time before his death at Fressingfield in Suffolk.