The Setons were granted the lands of Winton c.1152 by Scotland's King David I, which grant was re-confirmed in a charter to them, to Philip de Seton, from William the Lion in 1169.  Philip bestowed Winton on his 2nd son who thus became de Winton and who's descent Alan de Winton later married the heiress Margaret Seton. Alan's eldest son, William adopted his mothers surname and continued the line of the Seton's and became the 1st Lord Seton, his 2nd son, Henry de Wyntoun kept his father's name and founded the Winton's of Wrychthouses and who's grandson was the noted Scottish Chronicler.

Nevertheless, while the 3rd Lord Seton (the first to be named George, of five that were named George in succession after him) began the Castle of Winton, it was the 4th Lord Seton who completed the original Castle.  His taste for splendid buildings may have contributed to his embarrassments. "...He...erected the original house of Wintoun, which appears to have been destroyed in Lord Hertford's inroad. The historian of the family says, '(He) ...built the haill place of Wintoun, with the yard and gardens thereof,' and he describes quaintly its ornamented gardens, the flower-pots of which were surrounded by a hundred wooden towers or temples, surmounted by bells over-gilt with gold".

Winton Castle was the first in a series of structures built on the current spot which originally consisted of a tower house of four stories, with various out-buildings and a defensive curtain wall, which was necessary as Winton lay directly in the main travelling route, or invasion route, from England into Edinburgh. 

This castle however, was burnt by the English Earl of Hertford during the "Rough Wooing" in 1544, under orders of England's King Henry VIII and largely destroyed as a result.

One of the descriptions written from the English invaders was:

One of the greatest patrons of the ornamental arts, connected with the laying out of grounds and the creation of rural seats, was George Lord Seton. This accomplished nobleman, after having built Winton House, of whose splendour no traces now remain, added to it a garden, which contemporary historians describe as the wonder of the times; " erecting," in the words of a MS. history of the family of Winton, "about the knots of flowers five score torres of timber, of 2 cubits high, with two knops on their heads, the one above the other, each of them as great as a rouch bouell, overgilt with gold, and their shanks painted with divers oiled colours." MS Hist. of Family of Winton. See Pinkerton, vol. II.

The same Nobleman possessed another fair seat, called Castle Seton, which was destroyed in an incursion of the English. "The same nycht," says a laconic old historian, " we encampit at a toun of the Lord Seton's, where we brent and raised his cheif castll, called Seton, which was rycht fayre, and destroyed his orchards and gardens, which were the fayrest and best in order that we saw in all that countrye." Late Expeditioune in Scotland in 1544. Dalzel's Fragments.

Winton House as we now know, was then 1st rebuilt by Robert Seton, 1st Earl of Winton, using the remains of the older castle, and it was rebuilt again by his second son, George Seton, the 3rd Earl of Winton in the early 17th century, who created the house as it is now and added the embellishments that Winton House is known for, as a residence for his older brother Robert, 2nd Earl of Winton, who passed the Earldom to him at such an opportune time and age. 

While the 3rd Earl is given credit for work, it was in fact his older brother Robert, 2nd Earl who designed the layout and work, in conjunction with the King's Master Mason, William Wallace. 

Robert Seton himself, while being declared "insane or otherwise unfit" to maintain the Earldom, retired to occupying himself continually with the rebuilding designs for the Palace of Seton and Winton House, which was overseen and approved by George, 3rd Earl of Winton.

Previously Winton was a defensive structure, but the Earl's of Winton's work transformed the residence into a more palatial one.  As the Seton's were the custodians and tutors of King Charles I, Winton House then was another of the young Prince's early residences, and a favourite retreat after he returned and ascended to the Scottish throne. 

Architecturally, Winton is also one of the most important houses in Scotland. This is largely due to the work of William Wallace, the King's Master Mason who was responsible for adding the famous carved twisted chimneys and the beautiful plaster ceilings at the start of the Scottish Renaissance. 

As a result of Wallace's work, he was chosen as the Architect for Heriot's Hospital in Edinburgh, to which he continued the styles incorporate at Winton into the Heriot project.

From this period, Winton House was always used as the private retreat and entertaining house of the Seton's of Winton family:

The Earls of Winton, the Seton's of Barnes, St. Germains, Foulstruther, Whittingshame, Garleton, Olivestob and Windygoul all having use of the property.  While the latter four branches became extinct, the primary three remain.

The 4th Earl of Winton entertained significantly at Winton, and his 2nd son resided at Winton for most of his life, and had he lived to marry, it is likely that he would have founded a branch there.  It was however George, 5th Earl of Winton who was the last Seton of Winton.  He had only a few years to enjoy his tenure, following his return from France and the low countries after the death of his father years previous, where the Kingston and Garleton families had almost exclusive use until he returned and succeeded his father.

With the events of the rebellion of 1715, where the 5th Earl became engaged, the ages-old Seton-Winton Estate was forfeit to the Crown, although, the 5th Earl of Winton maintained communications with his tenants and quietly directed affairs over the years. 

It was found that during the rebellion of 1745, he directed to have the tenants care for the needs of Prince Charles Stuart while he and his army were encamped about, and the Prince rested briefly at Winton.

The family of the Seton's of Barnes, St. Germains and Garleton had made efforts to re-acquire the Estate, as male-heirs of the family, but were unsuccessful due to the want of funds.  However there remains to this day, significant interest in the Estate, by the remaining senior lines of the House, and the collateral junior branches.