Thomas Thornton (c.1541-1629) D.D. was an English Church of England clergyman and academic administrator.
Thornton received a Bachelor of Divinity degree followed by a Doctor of Divinity degree at Oxford University. He was based at Christ Church, Oxford and was a Canon of Christ Church Cathedral, Oxford. He was twice Vice-Chancellor at the University of Oxford during 1583–4 and 1599–1600.