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.  Winton House as we now know, was 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. 

Previously Winton was a defensive structure, but George, 3rd Eal 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 was another of the young Prince's early residences, and a favourite retreat after he ascended to the Scottish throne.  It was visited frequently by King Charles I, who was raised in his youth largely by the Earl of Winton's brother, Alexander Seton, 1st Earl of Dunfermline and Chancellor of Scotland, and who educated the future King at Seton Palace and Pinkie House.  Similary, Winton played host to King Charles II, and was the private, or personal, family home of the head of the Seton Family as a retreat from the rigors from the Palace of Seton.