In 1898 after Britain gained dominance in Sudan as part of a condominium arrangement, Lord Kitchener proposed founding a college in the memory of Gordon of Khartoum, who was killed in the Siege of Khartoum. The request for donations of £100,000 to build the college was achieved in six weeks and the Gordon Memorial College was founded in 1902 with initially three schools - an industrial school and two higher primary schools and a small teachers training centre.

By 1906, the college was also offering programs for training assistant engineers, land surveyors and primary school teachers. The first equipped laboratory for bacteriological analysis was added in 1905, with donations from Sir Henry Wellcome, an American-British pharmaceutical entrepreneur and archaeologist. There was also an affiliated Military school.

In 1924, it was decided to make the college a wholly secondary institution with the college incorporating programs in Sharia, engineering and surveying, education (teachers training), clerical work, accounting and science. Primary and military schools were removed. The Kitchener School of Medicine, the first medical school in Sudan, was also established that year.

Main building of Khartoum University. A palm lane leading up to the pointed arched entrance of a symmetrical building with galleries on two floors, 1961.

Dates for the establishment of further schools were; 1936 School of Law, 1938 School of Agriculture and Veterinary Science, 1939 Science and Engineering and 1940 Arts. In 1947, the college was affiliated with The University of London as the first overseas participant in its "special relationship" scheme. The first graduates to receive University of London degrees completed their programs in 1950. The next year, Gordon Memorial College was formally renamed University College Khartoum, which incorporated the Kitchener School of Medicine

When Sudan gained independence in 1956, the new Parliament passed a bill to award university status to Khartoum University College. It officially became Khartoum University on 24 July 1956. The eminent horticultural scientist John Pilkington Hudson was a visiting professor in 1961–1963, who founded its department of horticulture.[6]