In 1905 Sir Henry Wellcome donated a fully equipped laboratory for bacteriological analysis, thus began the fruitful association between Khartoum and the Welcome Research Laboratories. In 1924, the College developed into a vocational secondary school concentrating on teaching the following disciplines: Sharia, Engineering, Teachers' Training, Clerical Work, Accounting and Science. In the same year, Kitchener School of Medicine was established.

The year 1936 witnessed the beginning of higher education in Sudan with the establishment of the School of Law. By 1940 the College included schools of Agriculture, Arts, Law, Science, Engineering and Veterinary Science. Each school was attached to the government department in which the graduates would be expected to work.

In January 1945, all these schools were brought under one administration in a special arrangement with the University of London. The College was upgraded in 1951 to become Khartoum University College. In the same year, Kitchener School of Medicine was incorporated in the University College. The University of London set the examinations and awarded the degrees. The outstanding students were awarded bachelor's degrees from the University of London and the rest obtained College diplomas. The present University of Khartoum is the result of the natural transformation of the University College of Khartoum when the country became independent in 1956. The bill giving full University status to the College was passed by Parliament on 24th July 1956, since then, the University witnessed considerable expansion.