The objective of an emblem is to symbolise the university in manner and purpose, as countries do so with national flags. Many universities create emblems and mottoes with their birth. The creation of the University by law was as undramatic to those around, as the gradual change from adolescence to adulthood. The creation of an emblem to mark its new phase did not occupy the minds of its administrators and academics.

When the University acted as host to the Conference of Heads of African Universities in September 1963, there were many occasions indicating a 'show of the flag', which forcefully impressed the need for an emblem.

Ideas revolved around four features:

1. The Nile, the symbol of the great civilization of the Nile Valley, emerging from the junction of the White and Blue Niles to project the geographical location. This now figures as two converging lines - blue on the right hand and white on the left hand, and the double line of blue and white continuing upwards from the point of junction; at the same time the blue and white lines define the lower sides of an open book and the double line (the Nile) forms the spine.

2. Something to represent the modern development of education; this is projected by the drawing of the main University building, occupying the space between the blue and white 'Niles', with rays emerging from it to illustrate a black background - the dispersal of ignorance.

3. Something of the indigenous culture; this is shown by the rectangular tablet occupying the space between the Main Nile and the White Nile - on the left hand page of the open book. It is a diagram of a tablet of offering from the remains of the Meroitic Kingdom. The drawing is taken from Volume II (plate XLV no. 131) of F.L. Griffith's Meroitic Inscriptions: Napata to Philae and Miscellaneous published in 1912. The explanation given on page 56 of the book is "Tablet of the shape of a square table of offerings with the projection at the top in the shape of disc and horns of Isis". To the Meroitic, Isis was the mother of generations whose wisdom increased as more generations were born (the hope of the University). Prof. E.N. Dafalla, the second Sudanese Vice-Chancellor of the University, replaced the original inscriptions in the Meroitic tablet by the four Meroitic letters (right to left) "kh. r. t. m.".
The tablet of offering with the Meroitic letters and the head of Isis are meant to embody Dedication and Sacrifice as implicit in the offering, Challenge as posed by the still undisciplined Meroitic writing and the remains of that ancient Sudanese civilization of 725 B.C to 350 A.D which await discovery, and Wisdom as denoted by Isis, the mother of generations.

4. Now remains the motto which occupies the right hand page of the open book. It is in Arabic writing intended to reflect the dominant origin and culture of modern Sudan. It reads : Allah - al-hagiga - al-watan - al-insaniyya; God - Truth - Country - Humanity. The culmination of knowledge is the Omniscient God, the secrets of whose creation man has been and shall forever remain pursuing; the basis of knowledge is truth; the purpose is the elevation of man, our countrymen and fellow-men at large.

It began with some scribbling of diagrams in which Dr. E.N. Dafalla tried to put across some ideas that would serve as a label embodying some cultural heritage and moral values appropriate to a Sudanese University. The ideas revolved around the Nile as the home of ancient civilization, a 'loh', a traditional wooden tablet of characteristic shape for writing and learning the Koran, the outline of the map of Sudan with rays radiating from the center dispersing darkness, an outline of the old Gordon College which reflects modern education, an open book.

On March 1966, Dr. E.N. Dafalla had had an interview with Sayed Ibrahim El Salahi, a famous Sudanese painter, and explained the University's need for an emblem, which is explicit in meaning and simple to reproduce. In August Salahi presented ten productions that were examined, discussed and commented on at a tea party attended by the Vice Chancellor, Deans of Faculties, the Student Warden, Hostel Wardens and members of the Executive Committee of the Student Union. A historian pointed out that all the drawings presented lacked a symbol of indigenous Sudanese history and civilization, and thus the tablet of offering.

Salahi completed the work and the final product, the present emblem, was ready by December 1966.