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Thomas was the son of Robert, 1st Lord Boyd, who was a regent during the minority of King James III of Scotland. His father was able to have Thomas created Earl of Arran and Baron Kilmarnock in the Peerage of Scotland, and arrange for Thomas' marriage to Princess Mary Stewart of Scotland, sister of King James III and daughter of King James II of Scotland, in 1467. The marriage was unpopular, especially after Lord Boyd and his brother, Sir Alexander Boyd, were later convicted of treason for abducting young James III, contriving the marriage of Thomas to Princess Mary Stewart (which was considered as an unforgivable insult by King James III), and establishing the regency.