Thomas Winniffe (1576–1654) was an English churchman, the Bishop of Lincoln from 1642 to 1654.
He was born and baptised at Sherborne, Dorset, in 1576, the son of John Winniffe (1540?-1630), who was buried on 28 September 1630 in Lambourne church, Essex. He matriculated from Exeter College, Oxford, on 22 Feb. 1594, and was elected fellow in 1595; he graduated B.A. on 12 July 1598, M.A. on 17 May 1601, B.D. on 27 March 1610, and D.D. on 5 July 1610. In August 1605 he was one of those who disputed in moral philosophy before James I, his queen Anne of Denmark, and Henry Frederick, Prince of Wales on the occasion of their visit to Oxford.
On 5 May 1608 he was admitted to the rectory of Willingale-Doe, Essex, and on 15 June following to that of Lambourne in the same county, and on 30 June 1609 he resigned his fellowship at Exeter, having livings above the statutable value.
After Prince Henry's death Winniffe became chaplain to Prince Charles. However, on 7 April 1622, when the Spaniards were overrunning the Electorate of the Palatinate, Winiffe preached a sermon denouncing Gondomar, and comparing Spinola with the devil. Sent to the Tower of London, Winiffe repented and appealed to the Spanish and imperial ambassadors, whose intercession caused his release a few days later. On 17 September 1624 he was nominated dean of Gloucester, and was installed on 10 November. He remained chaplain to Charles after his accession, and on 8 April 1631 was nominated dean of St. Paul's in succession John Donne, who bequeathed him a picture; he was also one of the three to whom Donne is said to have left his religious manuscripts. The canons elected Winniffe dean of St. Paul's on 18 April; on 15 March 1634 he took the oath as an ecclesiastical commissioner.