Vice president of Kings’ College
For a second time, McCaul's fortunes were shaped by the ambitions of a new governor general. In 1842, Sir Charles Bagot took office and worked with Rev. Strachan to immediately open King's College, which had officially been granted a charter in 1827, but had not yet formally opened its doors. McCaul had expressed his interest to Bagot for a role at the new university, who decided to appoint him vice-president and professor of classics.
However, Bishop John Strachan, the founder of King's College, initially resisted, advocating recruiting someone from England, instead of appointing the Irish McCaul, writing:“if we are to commence King's College in an imposing, popular, and effective manner, the President and leading Professors must without exception be from England, and this I believe is now generally expected by a vast majority of the intelligent inhabitants of the Province.”Yet, Bagot remained sufficiently impressed by McCaul's qualifications and work at Upper Canada College that he dismissed Strachan objections.
McCaul set to work in 1843 to establish a new curriculum for the college. The curriculum was classical and elitist, very much aligned with McCauls’ own experience from Trinity College. While Strachan had originally put forward a more liberal Scottish-model of education, which emphasized universal access to education, his views had become more conservative following the Rebellion of 1837.
While vice-president, McCaul was aligned with the conservative majority on the faculty who supported the original 1827 Charter for King's College, which established the college as an Anglican institution. This was controversial, given Upper Canada was becoming a more religiously plural society. In 1845, McCaul wrote a lengthy treatise defending the college's status as an Anglican college under the pseudonym “A Graduate.”
In 1848, Strachan resigned as president and McCaul was appointed his successor. However, soon after, the government led by the reformist Baldwin abolished Kings’ College and established the non-sectarian University of Toronto. Strachan immediately went to work to establish Trinity College, which remained formally tied to the Church of England. McCaul choose to remain at the new University of Toronto as president until 1853. In 1853, he became president of a constituent college of the University of Toronto, University College, until his retirement in 1880.