Anjou. He returned to England on 13 July 1577.
During his absence Wilson was on 23 April 1577 nominated a commissioner for a special visitation of Oxford University, but he was destined for more important work. In September the Spanish ambassador wrote that Leicester, with a view to furthering his project of marrying the queen, was bringing into the council all his adherents, of whom Wilson was one (Cal. Simancas MSS. 1568–1579, p. 546). Wilson does not, however, occur as a privy councillor until 12 Nov., when he was sworn secretary of state in succession to Sir Thomas Smith (Acts P. C. ed. Dasent, 1577–8, p. 85). From that date he was constant in attendance on the council, but he was somewhat overshadowed by the superior ability of his colleague in the secretariate, Sir Francis Walsingham [q. v.], and the nature of his political influence is not easy to distinguish, more particularly as he tempered his adherence to Leicester with a firm desire to stand well with Burghley. He was, however, the principal authority on Portuguese affairs, and was the main supporter of Don Antonio's ambassadors in London (Cal. Simancas MSS. 1580–6, p. 183). In 1580 he became one of Elizabeth's lay deans, being installed dean of Durham on 5 Feb. 1579–80, a preferment for which he was a candidate in 1563, when William Whittingham [q. v.] was appointed (Le Neve, Fasti, iii. 299). Ralph Lever [q. v.] protested against Wilson's election (Cal. State Papers, Dom. 1547–80, p. 644), and the nomination of a layman to the deanery was a rude assertion of the royal supremacy against those who had cavilled at Wilson's predecessor on the ground of his invalid ordination (cf. Add. MS. 23235, f. 5).
Wilson's last attendance at the council board was on 3 May 1581. He died at St. Catherine's Hospital on 16 June following, and was buried there on the 17th. He ordered in his will that he should be buried ‘without charge or pomp,’ and no trace of his monument, if there was one, remains. A portrait of Wilson, dated 1575 but repaired in 1777, representing him in a black cap and dark furred dress, belonged in 1866 to Sir Thomas Maryon Wilson, bart. (Cat. First Loan Exhib. No. 214, where Wilson is erroneously styled ‘Sir Thomas’). Another, an old copy of an anonymous painting, was in 1879 transferred from the British Museum to the National Portrait Gallery, London. A copy of his will, dated 19 May 1581, is preserved at Hatfield (Cal. Hatfield MSS. ii. 391). He left his house at Edmonton to the overseers of his will, Sir Francis Walsingham, Sir William Winter, and Matthew Smith, to be sold to pay his debts; five hundred marks to his daughter Mary on her marriage or coming of age, and a like sum to his daughter Lucrece; his son Nicholas was to be sole executor. No successor was appointed to Wilson, Walsingham acting as sole secretary until Davison's selection on 30 Sept. 1586. His death was the occasion of various poetical laments (cf. Hist. MSS. Comm. 2nd Rep. App. p. 97, 4th Rep. App. pp. 252–4).
Wilson was twice married: first, to Jane, daughter of Sir Richard Empson [q. v.], and widow of John Pinchon of Writtle, Essex (Baker, Northamptonshire, ii. 141). By her Wilson appears to have had no issue; and he married, secondly, Agnes, daughter of John Winter of Lydney, Gloucestershire, sister of Sir William Winter, the admiral, and widow of William Brooke (Visit. Gloucestershire, 1623, p. 274); of her three children, the only son, Nicholas, settled at Sheepwash, Lincolnshire (see pedigree in Coll. of Arms MS. C. 23); Mary married, first, Robert Burdett (d. 1603) of Bramcote, by whom she was mother of Sir Thomas Burdett, first baronet, ancestor of Sir Francis Burdett [q. v.] and of the Baroness Burdett-Coutts; and, secondly, Sir Christopher Lowther of Lowther, Westmorland. She was buried in the choir of Penrith parish church (Lansd. MS. 982, f. 2). Wilson's second daughter, Lucrece, married Sir George Belgrave of Belgrave, Leicestershire.
Wilson has generally been confused with one or more contemporaries of the same name; a confusion of him with Sir Thomas Wilson (1560?–1629) [q. v.] has led to his being frequently styled a knight. Other contemporaries were Thomas Wilson (d. 1586), a fellow of St. John's College, Cambridge, who took refuge at Frankfurt during Mary's reign, was elected dean of Worcester in 1571, and died on 20 July 1586 (Cooper, Athenæ Cantabr. ii. 5–6); Thomas Wilson (d. 1615), canon of Windsor (see Lansd. MS. 983, f. 147); and Thomas Wilson (1563–1622) [q. v.]
