Waynflete was appointed Master of the school at Winchester in 1429 and stayed until 1442. In 1447, he became Bishop of Winchester, and in 1457 he founded Magdalen College, Oxford, and a school to provide it with scholars. He died in 1486, aged 88; his tomb can be found within the walls of Winchester Cathedral.

William Patten was known as William of Waynflete because in the middle ages it was customary for men to adopt as a surname their town of birth rather than their father's name. He was at one time, headmaster at Eton, and he also had some involvement in the building of Tattershall Castle.

After founding Magdalen College and the school in Oxford, he was determined to do something for his birth place, Wainfleet. He gave John Gygur, priest of Tattershall and warden of the college there, instructions to arrange for and supervise the building of the school. On April 25, 1484, Henry Alsbroke contracted with William of Waynflete to make the ceiling and floor. John Cowper is now generally acknowledged to have been the mason or designer. His work at Escher, Surrey and at Buckden Palace, Huntingdonshire (now Cambridgeshire), are in a similar brick style, all influenced by Tattershall, where he was working on the church.

Harris and Pevsner, in their book The Buildings of England - Lincolnshire have this to say about the school:

The W[est] front is flanked by broad three storied polygonal [should be octagonal] towers. Central doorway with depressed head, and above this a four light perp window. Entrances also to the towers. The long N[orth] front has six irregular bays of brick with moulded brick single and double lights and two projecting chimney flanks. The E[ast] front has no towers but a five light window. The great first floor room is still the original static oblong space. The wide splayed window recesses do not yet come down to the ground (Thornton Abbey). Two chimney pieces with castellated decoration and corbelled angel heads are blatantly and unashamedly Victorian Gothic.
It is not known how long the school took to be completed. It is not a particularly large building, and it is not as complex as Tattershall Castle, for which all building accounts still exist. There are no such accounts for the school; but there is a letter detailing the carpentry work involved, dated April 1484; and we know that work began soon afterwards. A letter sent to Waynflete by Gygur records initial discussions with suppliers of bricks and timber; Master Tontoft and John Robinson. A house on the site of the school had to be pulled down and some of its materials were suitable for reuse, but new timber was required for its floor and roof. Miraculously, the upper room floor beams constructed by Alsbroke have survived.

Bricks

The bricks have been laid in English Bond style, which was very popular during the Tudor period. On the west face which carries the two towers and the main entrance, the brickwork has a series of patterns which include coloured diapers and zig-zags for which special glazed bricks were used.

The north tower contains a spiral staircase, and like Tattershall castle, it has an inset moulded brick handrail. The 15th Century saw the biggest growth in the use of brick for buildings, especially in the Midlands. Bricks were cheap and could be produced wherever suitable clay existed, but considerable amounts of brush wood would be required for the firing, and this was often hard to get hold of. The complex details often obtained in brickwork were the result of very accomplished workmen and at that time represented a new range of skills.

Those responsible for new brick buildings from 1430 onwards were probably the most rich and powerful in the country. Among them were Henry VI at Eton college, Ralf Cromwell at Tattershall Castle, William of Waynflete at Esher Palace, Farnham Castle and Wainfleet School; and Bishop Rotherham of Lincoln at Buckden Palace. Within the period of 50 years many brick buildings were constructed by this small group; including schools, colleges, gate-houses and towers. Many of the buildings were designed to display the wealth and prestige of their builders. The members of this small group all knew each other and often employed the same masons. Masons became so powerful that they formed their own secret society: The Freemasons.

John Cowper gained experience at Tattershall Castle under a foreign master, he later worked at Esher palace for Bishop Rotherham. He is probably the designer of Waynflete school, which is partly based on Esher. He also appears in the 1480s at Kirkby Muxloe castle as a master mason. The red bricks for Wainfleet school are thought to have been transported by water from the Isle of Ely, though this is probably untrue. A vast quantity of plain bricks were required for walling (the laying of these was probably semi-skilled work). The creation of door and window mouldings, vaulting and staircases was highly skilled and required cut or moulded bricks, which would have to have been produced on site.

The walls are solidly built, meaning that there is no rubble in the middle, as was sometimes the case at that time. Specially cut bricks were used for the outer angles of the towers, axe marks can still be seen on some of these. Diaper patterning was used on the west wall with special bricks decorated with fused sand. The green shine would have contrasted well with the matte red wall. More traces of glazed bricks can be found on the east wall and the main chimney breast. Stone was used for the east and west windows and the door on the west front. For the other windows and doors, moulded bricks were used; these may have originally been covered with cement or plaster to give an appearance of expensive stone. The approximate size of the bricks used are 238-250mm x 112mm x 56-62mm.

Bonding in the Middle Ages was very irregular, but the Tudor period saw a consistent practice in the laying of bricks. They were mostly laid in alternating courses of stretchers (long sides) visible on the wall face, and headers (ends), visible. It has to be said that the laying of bricks in a regular fashion gives a more aesthetic overall appearance. English Bond later gave way to Flemish Bond.

At Foulkbourn in Essex, a huge brick tower of French design was built. In this tower was a spiral staircase with a moulded brick handrail.

At Eton College, founded by King Henry VI in 1440, brick was the main material used, although stone was used for the walls of the chapel. At Cambridge University, several colleges (Queens was the first) were being built in brick before the end of the 15th Century. Henry VIII's Hampton Court Palace was, at that time, the largest house in England to be built of brick. Ralf Cromwell's master brick maker at Tattershall was a German, brought over especially for the job; but by the end of the century, English brick makers were given plenty of opportunity to prove their skills, with brick buildings becoming very popular.

The gate house of Esher Palace, now known as 'Waynflete Tower', is all that survives of another house built by William Waynflete around 1475-80, just a few years before the building of Wainfleet School. Waynflete Tower has a spiral staircase with reddish-brown headers and yet another moulded brick handrail. These staircase vaults, achieved mainly with stretchers, are extremely accomplished for such an early date.

Other buildings similar to Wainfleet school include The Deanery in Hadleigh, Suffolk, built using English Bond in 1495; it has two towers and some diaper work. Anne Boleyn's Gateway at Hampton Court Palace was built in 1520; the English bond was later modified for diaper work and the gateway was added to at a later date.

Uses of the Building

In the south tower, there is a pre-Reformation bell inscribed with the words Ave Maria Gra Sia Plena, which means 'Hail Mary Full Of Grace'. It hangs from a timber frame dated 1796. The bell could be heard ringing across the town summoning children to school, up until its closure in 1966. The upper room was originally used as a chapel; an altar stood beneath the east window, and the masters and scholars would pray there each day. The altar was later replaced by a large wooden desk which remained until 1966. The old chapel provided the largest classroom. The walls are wooden panelled, which is not original. The hammer-beam roof is supported by Victorian corbels and has carved bosses at its intersections and these were repainted in the 1950s by local artist, Ernest E Turner, which really brought the craftsmanship back to life.

The 18th-century glass of the perpendicular east and west windows is inscribed with the lilly motif of Wainfleet's coat Of arms. The carved fireplaces carry the Magdalen arms and the legend Sicut Lilium ('In the same way as the lily').

The original classroom was downstairs, along with the Master's quarters. When the school first opened, there was a single master and probably about seven pupils.

England, around this time, was suffering through the Civil War, and the walls around the lower windows were fitted with stout hooks so that heavy shutters could be hung there in emergencies; the towers were built with fortress-like slit windows. The school was actually used as a fortress during the Second World War. Soldiers were stationed there with a Bren Gun mounted on one of the towers.

The headmaster of the school was traditionally a clergyman, very often the Rector of the Parish. This position was often abused, though; some rectors appointed unqualified masters, and showed more interest in their salaries than in the school itself. This practice was corrected by the brothers John and Richard Pickburn who jointly held the headmastership. Their positive work was continued by SW Wilcox, in whose time the school had regularly to serve as the local church, whilst the present one was being built.

In 1877, when the reverend WM Gerish was head, there were only three pupils. He turned the school into a Grammar of very high standards; which remained until 1933, when it was closed and merged into the larger and newer buildings at Skegness, where it continues today.

Except for the war years, the school remained empty until 1951, when it was leased to Lindsay County Council and re-opened as a temporary Secondary Modern. In 1966, the school closed again and transferred to brand new premises on Magdalen Road. Shortly after in 1968, the building opened as a public library, occupying the whole of the ground floor. In 1993, the first floor was given over to the Magdalen Museum, now a registered charity, displaying articles and artifacts of local and national interest.

The school and its pupils in 1918-20. It shows just how far the school area extended in front of the school.The boys are enjoying a game of football, watched by the headmaster of the time, The Reverend William Gerrish.

The design of the school was unusual. This may be explained by John Gygur's suggestion that it could be in the style of Bishop Waynflete's palace at Esher, hence part chapel and part gate house.

The building is rectangular and measures 22.8m x 7.8m on the outside and 21m x 6m on the inside, excluding the towers. The east end has a large perpendicular 'five light window' similar to the west end's 'four light window' found above the main door. The two towers are divided into four stages by protecting drip courses, shown as string courses on the outside. The north and south sides have similar one and two light windows positioned irregularly. The two chimneys, enlarged in the 19th century, are on the north side. On the south side is a single, original, projection; which is now a cupboard. There is a vault beneath this which suggests that it might have been a garde robe. This fits in with the fact that part of the ground floor was used as the master's lodgings.

The school is now a Scheduled Monument and a Grade 1 listed building.