Sejarah universiti sebagai sebuah institusi akademik bermula pada 1824 dan berkait rapat dengan peranan Manchester sebagai bandar industri pertama dunia.[9] Ahli kimia Inggeris, John Dalton, bersama dengan ahli perniagaan dan industri Manchester telah mengasaskan Mechanics' Institute (kini UMIST) untuk memastikan para pekerja dapat belajar asas-asas sains. John Owens, seorang peniaga tekstil Manchester mewasiatkan £96,942 pada 1846 (kira-kira £5.6 juta pada 2005)[10] bagi menubuhkan sebuah kolej kepada golongan lelaki tanpa aliran. Pemegang-pemegang amanahnya menubuhkan Kolej Owens pada 1851. Kolej ini pada asalnya terletak di dalam sebuah rumah di persimpangan Quay Street and Byrom Street yang menjadi tempat tinggal seorang dermawan, Richard Cobden, dan kemudiannya menjadi tempat Mahkamah Kaunti Manchester. Pada 1873, kolej itu berpindah ke bangunan di Oxford Road, Chorlton-on-Medlock dan pada 1880, kolej itu menjadi kolej naungan Universiti Victoria. Universiti ini ditubuhkan dan dikurniakan Piagam Diraja pada 1880 lalu menjadi universiti awam pertama England. Universiti ini dinamakan semula sebagai Universiti Victoria Manchester pada 1903 dan menyerap Kolej Owens pada tahun berikutnya.[11]

By 1905 the two institutions were large and active forces in the area, with the Municipal College of Technology, the forerunner of the later UMIST, forming the Faculty of Technology of the Victoria University of Manchester while continuing as a technical college in parallel with the advanced courses of study in the Faculty.

Before the merger, the University and UMIST between them counted 23 Nobel Prize winners amongst their former staff and students. Manchester has traditionally been particularly strong in the sciences, with the nuclear nature of the atom being discovered at Manchester by Rutherford, and the world's first stored-program computer coming into being at the university. Famous scientists associated with the university include the physicists Osborne Reynolds, Niels Bohr, Ernest Rutherford, James Chadwick, Arthur Schuster, Hans Geiger, Ernest Marsden and Balfour Stewart. However, the university has also contributed in many other fields, such as by the work of the mathematicians Paul Erdős, Horace Lamb and Alan Turing; the author Anthony Burgess; philosophers Samuel Alexander, Ludwig Wittgenstein and Alasdair MacIntyre; the Pritzker Prize and RIBA Stirling Prize winning architect Norman Foster and the composer Peter Maxwell Davies all attended, or worked in, Manchester. Well-known figures among the current academic staff include author Martin Amis, computer scientist Steve Furber, literary critic Terry Eagleton, economist Richard Nelson[12] and biochemist Sir John Sulston, Nobel laureate of 2002.

In 2004, the Victoria University of Manchester (established in 1851) and the University of Manchester Institute of Science and Technology (established in 1824) were formally merged into a single institution.

The university today

The newly merged University of Manchester was officially launched on 22 October, 2004 when the Queen handed over the Royal Charter. It has the largest number of full time students in the UK, unless the University of London is counted as a single university. It teaches more academic subjects than any other British university. The President and Vice-Chancellor of the new university is Alan Gilbert, former Vice-Chancellor of the University of Melbourne, who has announced that he shall retire at the end of the 2009-2010 academic year.[13] One of his stated ambitions for the newly combined university is to 'establish it by 2015 among the 25 strongest research universities in the world on commonly accepted criteria of research excellence and performance'.[14] Manchester has the largest total income of all UK universities, standing at £637 million as of 2007.[6] Its research income of £216 million is the fifth largest of any university in the country.