In April 1853 Governor Hotham selected a University Council of twenty members, comprising government officials, clergy and professionals, about one third of whom were graduates of British universities. They were charged with the governance of the University under the leadership of a Chancellor, who was until 1934 also the chief executive officer of the University. The Council first met on 3 May 1853. At its second meeting, on 17 May 1853, the University Council resolved that an application be made to the Lieutenant Governor "to sanction the advance of L100, to be lodged to the credit of the Chancellor of the Melbourne University, in the Bank of Victoria, to meet the current expenses of the Council". The account was opened on 17 June. On 26 September 1853 the Council resolved that its Statute and Correspondence Committee be empowered to correspond with Sir John Herschel, Professor Malden, Professor Airy, Robert Lowe, M.P. and Chief Justice Sir W. a'Beckett on the choice of the first four Professors. On 10 April the following year the Correspondence Committee reported the text of letters sent, setting out requirements for the guidance of the English selection committee and on 27 December 1854 the Chancellor read Sir John Herschel's letter of 28 August announcing the appointment of H.E. Rowe (Classics), W.P. Wilson (Mathematics), F. McCoy (Natural Science) and W.E. Hearn (Modern History and Literature, Political Economy and Logic). All were in Melbourne by the commencement of lectures in April 1855 except Rowe, who died shortly after arrival, and was in due course replaced by M.H. Irving. New Professors were appointed as teaching diversified and former professors died or retired.

Faculties were established, each with a Dean at its head, in 1873 (Law), 1876 (Medicine), 1889 (Engineering), 1903 (Arts and Science) and later Veterinary Science, Agriculture, Education, Music, and Applied Science. In October 1903 University Statute IV ("The Faculties") was amended to provide, inter alia, that the Dean's duties include the obligation to "report to the Council at its October meeting in each year as to the character of the work being done in his Faculty."

Over time, the range of groups represented on Council has widened, and its numbers increased, but its role in overseeing all aspects of University life, developing policy, appointing staff, planning new academic developments (in consultation with the Professorial (later Academic) Board), pursuing a building program, managing the budget and promoting the interests of the University generally has remained essentially the same.

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