The public and private education systems inherited by the government after freedom were designed more to offer civil servants and professionals to serve the colonial administration than to educate the Sudanese. Moreover, the distribution of facilities, staff, and enrollment was biased in favor of the needs of the administration and a Western curriculum. Schools tended to be clustered in the vicinity of Khartoum and to a lesser extent in other urban areas, although the population was predominantly rural. This concentration was found at all levels but was most marked for those in situations beyond the four-year primary schools where instruction was in the vernacular. The north suffered from shortages of teachers and buildings, but education in the south was even more insufficient. During the condominium, education in the south was left largely to the mission schools, where the level of instruction proved so poor that as early as the mid-1930s the government imposed provincial education supervisors upon the missionaries in return for the government subsidies that they sorely needed. The civil war and the ejection of all foreign missionaries in February 1964 further diminished education opportunities for southern Sudanese.

Education is free and compulsory in Sudan between the ages of 6 and 13. In the 1996 school year 3 million pupils attended elementary schools, and 405,600 students were listed in secondary schools and vocational institutions. Institutions of higher education include the University of Khartoum,Omdurman Islamic University, the University of Juba , and the College of Fine and Applied Art,located in Khartoum.