In the matter of academic organisation Thomson was strongly in favour of reform. He disapproved of the principles on which college fellowships were then filled. At that period they were nearly all confined to persons born in particular districts, and at Queen's College, contrary to the statutes, elections were restricted to natives of Cumberland and Westmoreland. In conjunction with another fellow, George Henry Sacheverell Johnson [q. v.], Thomson endeavoured to remedy this state of things. In 1849 the fellows rejected the candidature of Mr. Goldwin Smith, afterwards regius professor of modern history, and elected instead a native of Cumberland whom they had previously removed from the list of expectants on account of his insufficient attainments. Thomson appealed against this action to Lord John Russell, the prime minister; in consequence of this and other representations a commission was appointed in 1850 to inquire into the constitution and revenues of the university, and in 1854 a second commission was empowered to revise the statutes of the university and of the colleges and halls. The proposed innovations alarmed the more conservative members of the university, and several attacks on the commissions appeared. In reply to one of these, entitled ‘The Case of Queen's College’ (Oxford, 1854, 8vo), by the Rev. John Barrow, D.D., Thomson penned ‘An Open College best for all’ (Oxford, 1854, 8vo). This pamphlet was generally considered the ablest contribution to the reformers' side of the controversy, and was largely quoted in the parliamentary debates.
In 1855 Thomson married, and, losing his fellowship in consequence, was presented by the crown to the rectory of All Souls', Marylebone. Within a few months, however, on the death of the Rev. John Fox, D.D., on 11 Aug., Thomson was elected provost of Queen's College and resigned his living. As provost he steadily pursued his liberalising policy. He advocated the enlargement of the curriculum of university studies, and, with a view to aiding scientific study, was one of the projectors of the university museum, which was afterwards erected in the parks. Outside Oxford he accepted preferment, whereby he extended his reputation as a preacher who appealed to the intellect rather than to the emotions of his audience. In 1858 he was elected to the preachership of Lincoln's Inn, and in 1859 he was appointed chaplain in ordinary to the queen.
Thomson's theological position was conspicuously defined during the controversy that followed the issue in 1860 of the ‘Essays and Reviews.’ In his ardour for reform at Oxford he had associated himself with Benjamin Jowett and the newer school of broad churchmen, and in 1855 he had contributed a paper on ‘Crime and its Excuses’ to ‘Oxford Essays.’ But when, in 1860, Jowett and his friends enunciated more daring theological opinions in ‘Essays and Reviews,’ Thomson severed himself from them, and in 1861 edited in reply a volume of essays, entitled ‘Aids to Faith’ (London, 8vo). The volume included contributions from Edward Harold Browne, Frederick Charles Cook, Charles John Ellicott, and Henry Longueville Mansel, besides an article of his own on ‘The Death of Christ,’ which was substantially a restatement of his Bampton lectures in more popular form. ‘Aids to Faith’ was the best general answer which ‘Essays and Reviews’ called forth, and possesses historical value as a clear statement of the orthodox position at that period. Almost at the same time Thomson was engaged, as one of a committee of ten, in preparing the ‘Speaker's Commentary,’ to which he contributed the ‘Introduction to the Synoptical Gospels,’ probably the best treatise on the subject then extant.
In the same year (1861), on the translation of Charles Thomas Baring [q. v.] to the see of Durham, Thomson, whose established fame as a preacher marked him out for promotion, was appointed Baring's successor in the see of Gloucester and Bristol. Within ten months of his consecration, however, Charles Thomas Longley [q. v.], the archbishop of York, was translated to Canterbury, and, though so junior a bishop, Thomson was appointed Longley's successor. He was enthroned at York Minster on 26 March 1862, and entered on an archiepiscopate which extended over twenty-eight years.
Thomson performed the various duties incident to his office with eminent success. From the commencement of his archiepiscopate he realised that, to keep its place in English life, the English church must show itself able to meet modern needs. He was active in his support of diocesan conferences and church congresses, and showed a keen interest in social, economic, and political questions, together with a just discernment of their relation to ecclesiastical matters. He made his first public appearance as archbishop at a meeting of the Castle Howard Reformatory in 1863, and from that time onwards he was present at every considerable public meeting in the diocese, whether its object was the amendment of the criminal law, the amelioration of the state of the poor, the encouragement of education, or the cultivation of art or science.
