William Holt (1545–1599) was an English Jesuit.
Holt was born at Ashworth in Lancashire. He was educated at home, and entered Brasenose College, Oxford, in 1563, took the degree B.A. in 1566, was elected fellow of Oriel College on 29 February 1568, and preceded to the degree of M.A. in 1572. In 1573, he was incorporated M.A. at Cambridge.
His studies led him to dissatisfaction with religious affairs in England. In 1574 he left Oxford and was admitted into the English College, Douai where he continued his theological studies till 1576, when he was ordained and sent to Rome to help in the establishment of the English College, Rome. He entered the Society of Jesus on 10 November 1578. In 1581 he was sent to England to help in carrying out the work which had been begun by Robert Parsons and Edmund Campion. He was sent by Parsons on a mission to Scotland, together with William Crichton at the end of 1581. Their object was to open up communications with Esmé Stewart, 1st Duke of Lennox, procure the conversion or deposition of the young James VI, and send information to Mary and Philip II of Spain through the Spanish ambassador Mendoza. Holt further communicated with Henry I, Duke of Guise and in May 1582 had an interview with him in Paris.
Elizabeth meanwhile had sent to Scotland Robert Bowes to counteract the influence of Lennox, and guard against the intrigues of the Jesuits in the Scottish court. In March 1583, Bowes prevailed on the king to authorise the arrest of Holt at Leith as he was on the point of setting out for France. Holt, who passed under the name of Peter Brereton, was kept for a time in Bowes's custody, and the letters found on him were forwarded to Francis Walsingham. But James VI soon took him into his own hands, and ordered him to be imprisoned in Edinburgh Castle, while Elizabeth demanded his surrender as an English subject, and asked that he should be put to the torture and compelled to confess. William Allen thought that Holt was tortured and withstood the ordeal with constancy; but Bowes's letters lead to the conclusion that torture was only threatened. James VI was himself concerned in some of Holt's intrigues. At the end of June the king recovered his liberty from Gowrie, took matters into his own hands, and negotiated for French and Spanish help in an invasion on England. To rid himself of Bowes's importunity about Holt, James allowed him to escape from Edinburgh Castle on 16 July, and took credit with the Duke of Guise for doing so. Holt sought refuge for a time in Flanders, and visited the college at Rheims. In 1585 he returned to Scotland to work in behalf of Mary, and was harboured by George Gordon, 6th Earl of Huntly in the north,