The Al-Qurba (Eastern Command) and the 6th Division were in Al-Fashir, Darfur (Western Command). The 1st Division was in Juba (Southern Command), and the 7th Armored Division was in Al-Shagara, south of Khartoum (Khartoum Command). The Airborne Division was at Khartoum Airport, and the 3rd Division was located in Khartoum city.

Despite the lack of primary military units allocated to it, the overall structure included a liaison officer attached to the General Command in Khartoum to facilitate communication between the division and various command elements. This organizational structure did not provide an accurate picture of the actual troop deployment. The 6th Division in Darfur was a reorganized brigade consisting of only 2,500 men. The strength of the units varied widely, with most brigades comprising 1,000 to 1,500 soldiers.

To reduce the pressure on the regular armed forces, the Sudanese government extensively utilized militias. During the reign of Al-Mirghani, there were what were known as "friendly forces," mostly of the Nuer ethnicity. During the time of Al-Sadiq Al-Mahdi, the government began forming militias under the name "Al-Marahil," and foreign influence also began to enter the country through the Libyan-loyal Islamic Legion forces in Darfur, with the tacit approval of the then-government of Al-Sadiq Al-Mahdi.

Under the Salvation regime, the same endeavor continued, with the government establishing popular defense militias for the army, such as the Popular Defense Forces. In the South, the army allied with the South Sudan Defense Forces, which were formed from seven groups after the signing of the Khartoum Peace Agreement with the Islamic National Front in 1997. They were led by the former Dean of Khartoum University, Dr. Riek Machar, in addition to some tribal militias in the South (such as the Tubu, etc.).

Later, the Bashir government replaced the Popular Defense Forces with more effective forces in the Darfur war when it established the Border Guard Forces and later the Rapid Support Forces during the Darfur war.

Military conflicts in which the Sudanese army participated:

The army and its allied militias fought in the following conflicts:

1. The Sudanese Civil War with South Sudan, 1955-2005. 2. The Darfur conflict, 2003-present. 3. The conflict between Sudan and the Sudan People's Liberation Movement - North, 2011-present. 4. The border dispute between South Sudan and Sudan in 2012. 5. The Arab-Israeli Wars, 1948, 1967, 1973. 6. The Iran-Iraq War, 1979-1988.