In 1429, Waynflete became headmaster of Winchester College, a position which he held until 1441.

During this time, Waynflete was appointed by Bishop Beaufort to the mastership of St Mary Magdalen's Hospital, a leper hospital on St Giles Hill, just outside the city of Winchester.
The first recorded headmaster after the foundation of the college, John Melton, had been presented by William of Wykeham to the mastership of this hospital in 1393 shortly before his retirement.

On 3 July 1441 Henry VI went for a weekend visit to Winchester College to see the school for himself.
Here he seems to have been so much impressed with Waynflete that by the autumn Waynflete had ceased to be headmaster of Winchester.
In October he was dining in the hall there as a guest, and at Christmas 1442 he received a royal livery, five yards of violet cloth, as provost of Eton.

Under the influence of Archbishop Chichele (who had himself founded two colleges in imitation of Wykeham); Thomas Bekynton, the king's secretary and privy seal; and other Wykehamists, Henry VI, on 11 October 1440, founded, in imitation of Winchester College, a college in the parish church of Eton by Windsor (not far from his own birthplace) called the King's College of the Blessed Mary of Eton by Windsor, as a sort of first-fruits of his taking the government on himself.
The college was to consist of a provost, 10 priests, 6 choristers, 25 poor and needy scholars, 25 almsmen and a magister informator (later "headmaster") to teach (Latin) grammar to the foundation scholars and to all others coming from any part of England, at no cost.
On 5 March 1440/41, the king endowed the college with some £500 a year taken from the alien priories: almost exactly the amount of the original endowment of Winchester.

Though reckoned first headmaster of Eton, there is no definite evidence that Waynflete acted as such.
The school building was not begun until May 1442.
William Westbury left New College, Oxford in May 1442, transferring himself to the king's service.
He appears in the first extant "Eton Audit Roll 1444–1445" as magister informator, and was probably such from May 1442.
If Waynflete was headmaster from October 1441 to May 1442, his duties must have been little more than nominal.
As Provost, Waynflete procured the exemption of the college from archidiaconal authority on 2 May, and made the contract for completion of the carpenter's work on the eastern side of the quadrangle on 30 November 1443.

On 21 December 1443 Waynflete was sworn to observe the statutes by Bishop Bekynton and the Earl of Suffolk, the king's commissioners, and he himself administered the oath to the other members of the foundation: then only five fellows and eleven scholars over 15 years of age. (
Younger scholars were not required to take an oath.)
It is said that he took half the Fellows and scholars of Winchester College to Eton to start the school there.
However, only five scholars and perhaps one commoner (pupil not on the foundation) left Winchester for Eton in 1443, probably in July, just before the election.
Three of them were admitted scholars of King's College, Cambridge on 19 July.
That college, by its second charter of 10 July 1443, had been placed in the same relation to Eton that New College bore to Winchester: i.e. it was to be recruited entirely from Eton.

The chief part of Waynflete's duties as Provost was the financing and completion of the buildings and establishment.
The number of scholars was considerably increased by an election of 25 new foundation scholars on 26 September 1444.
The college's annual income was then £946, of which the king contributed £120 and Waynflete £18, or more than half his stipend of £30 a year.
The full number of 70 scholars was not filled up until Waynflete's last year as Provost, 1446–1447 (Eton Audit Roll).
In 1429, Waynflete became headmaster of Winchester College, a position which he held until 1441.
During this time, Waynflete was appointed by Bishop Beaufort to the mastership of St Mary Magdalen's Hospital, a leper hospital on St Giles Hill, just outside the city of Winchester. The first recorded headmaster after the foundation of the college, John Melton, had been presented by William of Wykeham to the mastership of this hospital in 1393 shortly before his retirement.
On 3 July 1441 Henry VI went for a weekend visit to Winchester College to see the school for himself. Here he seems to have been so much impressed with Waynflete that by the autumn Waynflete had ceased to be headmaster of Winchester. In October he was dining in the hall there as a guest, and at Christmas 1442 he received a royal livery, five yards of violet cloth, as provost of Eton.
Under the influence of Archbishop Chichele (who had himself founded two colleges in imitation of Wykeham); Thomas Bekynton, the king's secretary and privy seal; and other Wykehamists, Henry VI, on 11 October 1440, founded, in imitation of Winchester College, a college in the parish church of Eton by Windsor (not far from his own birthplace) called the King's College of the Blessed Mary of Eton by Windsor, as a sort of first-fruits of his taking the government on himself. The college was to consist of a provost, 10 priests, 6 choristers, 25 poor and needy scholars, 25 almsmen and a magister informator (later "headmaster") to teach (Latin) grammar to the foundation scholars and to all others coming from any part of England, at no cost. On 5 March 1440/41, the king endowed the college with some £500 a year taken from the alien priories: almost exactly the amount of the original endowment of Winchester.
Though reckoned first headmaster of Eton, there is no definite evidence that Waynflete acted as such. The school building was not begun until May 1442. William Westbury left New College, Oxford in May 1442, transferring himself to the king's service. He appears in the first extant "Eton Audit Roll 1444–1445" as magister informator, and was probably such from May 1442. If Waynflete was headmaster from October 1441 to May 1442, his duties must have been little more than nominal. As Provost, Waynflete procured the exemption of the college from archidiaconal authority on 2 May, and made the contract for completion of the carpenter's work on the eastern side of the quadrangle on 30 November 1443.
On 21 December 1443 Waynflete was sworn to observe the statutes by Bishop Bekynton and the Earl of Suffolk, the king's commissioners, and he himself administered the oath to the other members of the foundation: then only five fellows and eleven scholars over 15 years of age. (Younger scholars were not required to take an oath.) It is said that he took half the Fellows and scholars of Winchester College to Eton to start the school there. However, only five scholars and perhaps one commoner (pupil not on the foundation) left Winchester for Eton in 1443, probably in July, just before the election. Three of them were admitted scholars of King's College, Cambridge on 19 July. That college, by its second charter of 10 July 1443, had been placed in the same relation to Eton that New College bore to Winchester: i.e. it was to be recruited entirely from Eton.
The chief part of Waynflete's duties as Provost was the financing and completion of the buildings and establishment. The number of scholars was considerably increased by an election of 25 new foundation scholars on 26 September 1444. The college's annual income was then £946, of which the king contributed £120 and Waynflete £18, or more than half his stipend of £30 a year. The full number of 70 scholars was not filled up until Waynflete's last year as Provost, 1446–1447 (Eton Audit Roll).
William Waynflete