He was the grandson of the previous earl, Sir Malcolm Fleming, through the latter's only son John (d. 1351).
Thomas subsequently had grave financial problems, probably due to the ransom he had to pay the English crown to be released.
In 1367, Thomas was regranted the earldom, but was stripped of the rights of regality enjoyed by his grandfather.
Thomas sold the earldom to Archibald the Grim, Lord of Galloway, later Earl of Douglas, in 1372.
The Douglases were, moreover, much more successful than the Flemings at crushing resistance to the Bruce dynasty in the south-west.