Thomas Wotton was born in 1521 at Bocton or Boughton Place, in the parish of Boughton Malherbe, in the county of Kent, and succeeded his father, Sir Edward Wotton, in that estate in 1550. He was appointed sheriff of the county of Kent in the last year of Queen Mary, and in July 1573 he entertained Elizabeth and her court at his residence, Bocton Place, when she offered him knighthood, which he declined. Wotton was twice married. By his first wife, Elizabeth, daughter of Sir John Rudstone, he had three sons: Edward, knighted by Elizabeth, and afterwards raised to the peerage as Baron Wotton by James I.; and James and John, who were also made knights by Elizabeth. His second wife was Eleanora, daughter of Sir William Finch of Eastwell in Kent, and widow of Robert Morton, Esq., of the same county, by whom he had a son, Henry, the poet and statesman, who was knighted by James I. He died in London on the 11th of January 1587, and was buried in the parish church of Boughton Malherbe, where a monument was erected to his memory.

Wotton was celebrated for his hospitality, and was much beloved and respected by all who knew him. He was also a patron of learning, and possessed a fine and extensive collection of books, remarkable for their handsome bindings. They are generally ornamented in a style similar to that used on the volumes bound for Grolier, whose motto he adopted. Although the majority of the bindings executed for him bear the legend THOMAE WOTTONI ET AMICORVM as the only mark of their ownership, they are sometimes impressed with his arms.

Izaak Walton, in his Life of Sir Henry Wotton, states that Thomas Wotton 'was a gentleman excellently educated, and studious in all the liberal arts, in the knowledge whereof he attained unto great perfection; who though he had—besides those abilities, a very noble and plentiful estate, and the ancient interest of his predecessors—many invitations from Queen Elizabeth to change his country recreations and retirement for a court life:—offering him a knighthood, and that to be but as an earnest of some more honourable and more profitable employment under her; yet he humbly refused both, being a man of great modesty, of a most plain and single heart, of an ancient freedom, and integrity of mind.'