A peace treaty was signed between Muslim Egypt and Christian Sudan called the Baqt, lasting centuries.

After the Egyptian-Ottoman Wars from 1831 to 1841, Egypt became an autonomous tributary state of the Ottoman Empire, governed by the Muhammad Ali Dynasty.

During this time period, British involvement in Egyptian grew, forming an Anglo-French debt commission that assumed responsibility for managing Egypt's fiscal affairs, that eventually forced Isma'il Pasha to abdicate in favor of his more pro-British son, Tawfiq Pasha.

A Sudanese religious leader Muhammad Ahmad declared himself the Mahdi and revolted against Egyptian rule.

Though Gordon was to organize the evacuation of Sudan, he found himself in the siege of Khartoum by Mahdist forces, eventually leading to his death.

The Condominium Agreement of January 19, 1899 provided for a joint administration of the Sudan by the British and Egyptian governments.

The supreme civil and military command of the Sudan was vested in the governor-general, who was nominated by the British government.

[14][15] This rivalry led to the rise of Sudanese elites who tended to split into anti-Egyptian and anti-British factions.

[20][21][22] In the 1953 Sudanese parliamentary election, Ismail al-Azhari's NUP received a majority of seats in parliament.

Despite winning a majority in the elections, Azhari realized that popular opinion had shifted against an Egyptian-Sudan union.

[23] Azhari, who had been the major spokesman for the "unity of the Nile Valley", therefore reversed the NUP's stand and supported Sudanese independence.

[24] On December 19, 1955, the Sudanese parliament, under Azhari's leadership, unanimously adopted a declaration of independence that became effective on January 1, 1956, creating the Republic of the Sudan.

Nimeiry adopted a pro-Arab nationalist political position, including signing the Tripoli Charter with the UAR and Libya, declaring the coordination of policies.

[14] Since 2000 Sudan had begun expressing an interest in changing the terms of the agreement so that it would be able to use a larger percentage of the flow.

[14] Seven of the eight other riparian states—Burundi, the Democratic Republic of the Congo, Ethiopia, Kenya, Rwanda, Tanzania, and Uganda—also pressed for a revised water allocation formula.

[14] While Egypt and Sudan generally agreed on the Nile water question, they had failed to resolve a longstanding dispute over the location of their border near the Red Sea, an area called the Hala'ib Triangle.

Sadat's successor, Hosni Mubarak visited Sudan in 1985 after a military coup overthrew Nimeiry that year.

[14] The relationship reached its nadir in 1995, when elements of the Sudanese government were complicit in a plot by an Egyptian terrorist group, Gama'a Islamiyya, to assassinate Egypt's president, Hosni Mubarak, while he was en route from the Addis Ababa airport to an Organization of African Unity (now African Union) summit in Ethiopia's capital.

[35] By the end of 1999, Egyptian anger toward Sudan had subsided, and President al-Bashir visited Egypt, where the two leaders agreed to normalize diplomatic relations.

[14] There has been cooperation on counterterrorism and development projects drawing water from the Nile, and the two governments agreed to establish a free-trade zone along the Egypt–Sudan border, where they would exchange commodities free of duty.

[14] By 2010 Egyptian–Sudanese relations were better than they had been in many years, although several long-term contentious issues, such as the future status of South Sudan, ownership of the Hala’ib Triangle, and use of Nile water, remained unresolved.

[36] Salva Kiir visited Cairo in 2009, when Egypt made clear it would accept the results of the January 2011 referendum on secession.