He was born at Kinnaird Castle near Brechin around 1490, the son of John Carnegie and his wife Euphame Strachan.
His father was killed at the Battle of Flodden (9 September 1513) and his mother died a month after (possibly grief-stricken).
In the autumn of 1548 Carnegie was the diplomat, sent with an armed guard, to deliver the ransom for the George Gordon, 4th Earl of Huntly who had been captured at the Battle of Pinkie Cleugh and was held in the Tower of London.
After leaving London he went to Blois in France with Archbishop Gavin Hamilton and the David Panter, Bishop of Ross to create the Regent Duke of Chatelherault.
Later that year, he was re-appointed, along with Sir Robert Bellenden, to the task of settling legal issues relating to the border.