During the reign of Queen Mary, his father, John Bodley, being obliged to leave the kingdom on account of his Protestant principles, went to live at Geneva. In that university, in which Calvin and Beza were then teaching divinity, young Bodley studied for a short time. On the accession of Elizabeth I he returned with his father to England, and soon after entered Magdalen College, Oxford. In 1563 he took his B.A. degree, and was admitted a fellow of Merton College. In 1565 he read a Greek lecture in hall, took his M.A. degree the year after, and read natural philosophy in the public schools. In 1569 he was proctor, and for some time after was deputy public orator.
Quitting Oxford in 1576, he made the tour of Europe; shortly after his return he became gentleman-usher to Queen Elizabeth; and in 1587, apparently, he married Ann Ball, a widow lady of considerable fortune, the daughter of a Mr Carew of Bristol. In 1584 he entered parliament as member for Portsmouth, and represented St German's in 1586. In 1585 Bodley was entrusted with a mission to form a league between Frederick II of Denmark and certain German princes to assist Henry of Navarre. He was next despatched on a secret mission to France; and in 1588 he was sent to the Hague as minister, a post which demanded great diplomatic skill, for it was in the Netherlands that the power of Spain had to be fought. The essential difficulties of his mission were complicated by the intrigues of the queen's ministers at home, and Bodley repeatedly begged that he might be recalled. He was finally permitted to return to England in 1596, but finding his preferment obstructed by the jarring interests of Burleigh and Essex, he retired from public life. He was knighted on April 18, 1604.
He is, however, remembered specially as the founder of the Bodleian at Oxford, practically the earliest public library in Europe. He determined, he said, "to take his farewell of state employments and to set up his staff at the library door in. Oxford." In 1598 his offer to restore the old library was accepted by the university. Bodley not only used his private fortune in his undertaking, but induced many of his friends to make valuable gifts of books. In 1611 he began its permanent endowment, and at his death, the greater part of his fortune was left to it. He was buried in the choir of Merton College chapel where a monument of black and white marble was erected to him.
Sir Thomas wrote his own life to the year 1609, which, with the first draft of the statutes drawn up for the library, and his letters to the librarian, Thomas James, was published by Thomas Hearne, under the title of Reliquiae Bodleianae, or Authentic Remains of Sir Thomas Bodley (London, 1703, 8vo).