(Alexander Nowell, a Marian exile, a fugitive from the "burning times" of Anglo-Italian policies, 1553–1558, was also a Protestant, Reformed and Anglican Churchman.)

[2] The marked ability with which he acquitted himself when presiding as "father of the philosophy act" at an academic commencement appears to have first brought him prominently into notice.

He also became known as an indefatigable student of the scriptures, the commentators, and the schoolmen, and was very early in his career singled out by John Whitgift, at that time master of Trinity, for marks of special favour.

In 1580 he was appointed by the crown to the regius professorship of divinity, to which Elizabeth shortly after added the chancellorship of St. Paul's, London, and from this time his position as the champion of the teaching of the Protestant and Reformed Church of England appears to have been definitely taken up.

In 1582, on taking part in a disputation at commencement, he took for his thesis, Pontifex Romanus est ille Antichristus, quern futurum Scriptura prædixit, or, The Roman Pope is that Antichrist which the Scriptures Foretold.

; and in 1593, on the mastership of Trinity College falling vacant by the preferment of Dr. John Still to the bishopric of Bath and Wells, he was an unsuccessful candidate for the post.

In the following year he published his De Authoritate Scripturæ, written in reply to Stapleton, prefixing to it a dedication to Whitgift (18 April 1594), the latter affording a noteworthy illustration of his personal relations with the primate, and also of the Roman controversialist learning of that time.

In May 1595 he was installed canon of Canterbury; but his professorship, mastership, and canonry appear to have left him still poor, and in a letter to Burghley, written about a fortnight before his death, he complains pathetically at being so frequently passed over amid "the great preferments of soe many."

He may possibly have been suffering from dejection at this time, owing to the disagreement with Whitgift in which, in common with others of the Cambridge heads, he found himself involved in connection with the prosecution of William Barret.

[2] The following is a list of Whitaker's published works:[2] Other works by Whitaker are extant in manuscript; the Bodleian Library has Commentarii in Cantica, and Prælectiones in priorem Epistolam ad Corinthios by him; Caius College, Theses: de fide Davidis; de Prædestinatione; and St. John's College, Cambridge, a treatise on ecclesiastical polity, which Baker thinks was probably from his pen, although it leans somewhat to Erastianism.