He was the son of Sir John Kerr of Ferniehirst and Katherine Kerr. His sister Margaret married
Lord Hay of Yester and was the mother of
William Hay, 6th Lord Hay of Yester. His homes were
Oxnam and
Ferniehirst Castle. In 1565 an agreement was made to end the vendetta between the Kerr family and the Scotts. It was agreed that there would be a number of marriages between the family members to end the feud. Everyone agreed to it, but not Thomas Kerr. Despite the families' intentions none of the marriages took place, but this was an important basis for Thomas's second marriage. A letter written by
Robert Constable in 1569 described how English and Scottish rebels drank ale played cards for "placks and hardheads" at Thomas Kerr's house in
Jedburgh. During the
Marian Civil War, Ferniehirst and his wife Jean were among the supporters of
William Kirkcaldy of Grange who lent him money on the security of the
jewels of Mary, Queen of Scots. In July 1575 he wrote from Paris to
Mary, Queen of Scots, describing the destruction of his houses with fire and gunpowder by English forces during the
Marian Civil War costing him at least 20,000 crowns, and the injuries sustained by his family and followers fighting for her cause in Scotland. He lost his jewels and the charters of his lands left in a coffer in
Edinburgh Castle which
Regent Morton confiscated. The
Earl of Angus cut down his woodlands.
Robert Melville was questioned about Mary's jewels. He said he did not know which pieces were held by Jean Scott, Lady Ferniehirst, but her friend, Margaret Learmonth, Grange's wife, would know. Ferniehirst was allowed to return to Scotland and was said to have watched the execution of
Regent Morton, wearing an outfit with conspicuous and extravagant cuffs. In June 1581
James Stewart, Earl of Arran tried to block the restoration and rehabilitation of Ferniehirst, who was considered guilty of taking "art and part" in the killing of the king's grandfather
Regent Lennox. However,
Esmé Stewart, 1st Duke of Lennox supported his return to favour and Ferniehirst knelt before the king for forgiveness in the garden at
Dalkeith Palace. The Scottish poet
William Fowler reported to
Francis Walsingham that the Laird of Ferniehirst had arrived secretly in London in May 1583, and was expected to go to France again. His second wife,
Janet/Jean Scott, was politically active. In October 1583 she wrote to Mary Queen of Scots from Ferniehirst with news from the Scottish court. She said she had been approached by the
Countess of Arran in person and by letter hoping that Mary would not join with the Hamiltons against her husband
James Stewart, Earl of Arran. She wanted Mary to advise her about this. She had forgotten to forward a letter from
Lord Seton. Mary was a godparent to one of her sons. Kerr was made a warden of the
Middle March of the Scottish border and keeper of
Liddesdale. In November 1584 the
Privy Council allotted him 100 troops and the use of
Hermitage Castle. He is buried in
Aberdeen but is memorialised in the Kerr family vault in the north transept of
Jedburgh Abbey. ==Marriage and children==