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 1569, and had, like himself, been brought up at Middleton school and Brasenose College, Nowell in 1572 endowed a free school at Middleton, to be called Queen Elizabeth's School, and to be under the government of the principal and fellows of Brasenose, and further founded thirteen exhibitions at the college to be held by scholars from that school, or from the schools of Whalley or Burnley, or in defect from any other school in the county. Moreover he put board floors in the lower rooms of the college, which had hitherto been unboarded. He was regarded as an authority on scholastic matters; revised the rules of the free school of the Skinners' Company at Tonbridge, Kent, and of the grammar school at Bangor, Carnarvonshire, and advised Parker with reference to the foundation of his grammar school at Rochdale. He is said to have been a benefactor to St. Paul's School (epitaph from plate in, History of St. Paul's; , Moderne Protestant Divines, p. 250), but the reference is probably to the school attached to the cathedral, not to Dean Colet's school (, Life of Colet, p. 159). He is also reckoned among the benefactors of Emmanuel College, Cambridge, but the nature of his benefaction seems uncertain.

Sitting as a member of the ecclesiastical commission in 1573, he signed the warrant for the arrest of Thomas Cartwright (1535–1603) [q. v.], and in 1574 was a commissioner for the trial of John Peters and Henry Turwert, two Flemish anabaptists who were burnt as heretics (Fœdera, xv. 740, 741). His name was included in the new commission for ecclesiastical causes of 1576 (Life of Grindal, p. 310). When Parker was at the point of death in May 1575, Nowell wrote to Burghley recommending Grindal, then archbishop of York, for the see of Canterbury (Cal. State Papers, u.s. p. 497). He also wrote to Burghley in 1576 begging him to take measures for the preservation of the college of Manchester, then in some danger from the conduct of the warden (Annals, ii. 68). When the college was refounded in 1578, Nowell's nephew, John Wolton, afterwards bishop of Exeter, was constituted warden, and Nowell himself one of the four fellows. In 1580 he received from the crown a license of absence from his deanery and rectory in order that he might visit the scholars of Brasenose and the school at Middleton, being commanded to inquire into the state of religion in Lancashire, and to preach on Sundays and holy days wherever he might be. His success in making converts from Romanism is said to have been recognised by the inclusion of his name in a list of those who, if the jesuit plots against the queen succeeded, were to be put to death (Annals, ii. 357). It was proposed that he should write an answer to the ‘Decem Rationes’ of Edmund Campion [q. v.], the jesuit, but that work was undertaken by his nephew, William Whitaker. However, in August 1581, when Campion was in the Tower, Nowell, with Day, then dean of Windsor and afterwards bishop of Winchester, held a disputation with him, a report of which was afterwards published (see below), and in 1582 he was named by the Privy Council as one of those fit to be employed to hold conferences with papists (Life of Whitgift, i. 198). An agent from Geneva having come to England to solicit help for his fellow citizens, he was directed by the council in January 1583 to apply to Nowell with reference to raising a fund (Life of Grindal, p. 415). In this year also the council placed the dean on a commission for the reformation of abuses in printing (Cal. State Papers, Dom. 1581–90, p. 115). John Towneley (1528?–1607), son of Nowell's mother by her second marriage with Charles Towneley, having been imprisoned at Manchester for recusancy, Nowell wrote to the council in March 1584 to beg that he might be sent to London, and that special care might be taken of his health (ib. p. 163; ). The queen having ordered Burghley to acquaint Archbishop Whitgift of her desire that Daniel Rogers, a layman, should be appointed treasurer of St. Paul's, Whitgift imparted the matter to Nowell, who besides joining in a petition to the queen from the chapter against the appointment, and representing its illegality to Rogers, wrote to Burghley on 1 Jan. 1585 beseeching him to intercede with the queen that she would abstain from violating the statutes of the church (Life of Whitgift, i. 443–8, where the letter is given). His intercession was effectual, for the dignity was conferred on Richard Bancroft [q. v.], afterwards archbishop of Canterbury. In this letter Nowell spoke of the deanery as likely soon to be vacant ‘by his extreme age and much sickliness.’ So, too, in 1588 he requested the council that he might not be troubled further about some business as he was weak and sickly (Cal. State Papers, u.s. p. 489). In that year having been collated to the first stall in St. Paul's instead of the less valuable stall which he had previously held, he resigned the rectory of Hadham. He preached at St. Paul's Cross on the defeat of the Armada before the lord mayor and aldermen on 20 Aug., and again when the Spanish flags were displayed on 8 Sept. In October the queen granted him