Although the present house of Manderston dates to the early 20th century and incorporates a Georgian mansion, it is built on the site of an old tower house.

By the 1240s the lands of Manderston were held by the Papedy or Pepdie family for the Earls of Dunbar. They are thought to have moved north from Islandshire in Northumberland and also held Dunglass by this time. Some time before 1247 Patrick, Earl of Dunbar, confirmed a grant of Manderston by Stephen Papedy to his brother, Thomas Papedy.

During the 14th century Nicola Pepdie, the heiress of Dunglass, married Sir Thomas Home of Home and it may be at this time that Manderston also passed to the Home family. Their second son, David, was granted the lands of Wedderburn in 1413 by Archibald Douglas, 4th Earl of Douglas, and from him the Homes of Manderston traced their ancestry.

Whether it was the Papedys or Homes who were responsible for building the first castle or tower at Manderston is not clear and neither is the form it took. The site occupies the southern end of a slight plateau amongst gently rolling countryside bounded to the west by Duns Law, to the north by the Whiteadder Water and to the south by the Blackadder Water. Immediately to the south of the house the land falls away steeply to an artificial pond created, possibly in the late 18th century, by damming Bells Burn which ran north-east past Edrom to join the Whiteadder.

In 1490 James IV confirmed the lands of Manderston amongst others to Alexander Home, 3rd Lord Home and Lord High Chamberlain of Scotland, and incorporated them into the barony of Home. Following Lord Home’s forfeiture James V granted half of the lands to Philip Nisbet of Nisbet and half to David Home of Wedderburn in 1517.

Alexander Home, de jure 5th Earl of Dunbar, who died in 1720 seems to have been the last Home to own Manderston and it had passed to the Swinton family of nearby Kimmerghame by the mid-18th century.

Around 1790 a new house was built for Dalhousie Watherston, which may have entirely replaced or incorporated the old tower house. Further work was carried out in 1870. Between 1901 and 1903 the then owner, Sir James Miller, 2nd Bt., commissioned the architect John Kinross to completely rebuild the house at any expense, whose family had made their fortune selling hemp and herring to Russia.

In 1950 Colonel Sir Gordon Palmer, later chairman of Huntley and Palmers Foods, married Lorna Bailie, daughter of Major Hugh Bailie who had inherited Manderston, and Manderston passed to the Palmer family. The current owner is Adrian Palmer, 4th Baron Palmer.