With the help of 10,000 Albanian troops provided by the Ottomans, Muhammad Ali purged Egypt of the Mamluks. In 1811 he launched a seven-year campaign in Arabia, supporting his suzerain, the Ottoman sultan, in the suppression of a revolt by the Wahhabi, an ultraconservative Muslim sect. To replace the Albanian soldiers, Muhammad Ali planned to build an Egyptian army with Sudanese slave recruits. 

Although a part of present-day northern Sudan was nominally an Egyptian dependency, the previous pashas had demanded little more from the kashif who ruled there than the regular remittance of tribute; that changed under Muhammad Ali. After he had defeated the Mamluks in Egypt, a party of them had escaped and had fled south. In 1811 these Mamluks established a state at Dunqulah as a base for their slave trading. In 1820 the sultan of Sannar informed Muhammad Ali that he was unable to comply with the demand to expel the Mamluks. In response the pasha sent 4,000 troops to invade Sudan, clear it of Mamluks, and reclaim it for Egypt. The pasha's forces received the submission of the kashif, dispersed the Dunqulah Mamluks, conquered Kurdufan, and accepted Sannar's surrender from the last Funj sultan, Badi IV. The Jaali Arab tribes offered stiff resistance, however.  Initially, the Egyptian occupation of Sudan was disastrous. Under the new government established in 1821, which was known as the Turkiyah or Turkish regime, soldiers lived off the land and exacted exorbitant taxes from the population. They also destroyed many ancient Meroitic pyramids searching for hidden gold. Furthermore, slave trading increased, causing many of the inhabitants of the fertile Al Jazirah, heartland of Funj, to flee to escape the slave traders. Within a year of the pasha's victory, 30,000 Sudanese slaves went to Egypt for training and induction into the army. However, so many perished from disease and the unfamiliar climate that the remaining slaves could be used only in garrisons in Sudan. 

As the military occupation became more secure, the government became less harsh. Egypt saddled Sudan with a parasitic bureaucracy, however, and expected the country to be self- supporting. Nevertheless, farmers and herders gradually returned to Al Jazirah. The Turkiyah also won the allegiance of some tribal and religious leaders by granting them a tax exemption. Egyptian soldiers and Sudanese jahidiyah (slave soldiers; literally, fighters), supplemented by mercenaries recruited in various Ottoman domains, manned garrisons in Khartoum, Kassala, and Al Ubayyid and at several smaller outposts. The Shaiqiyah, Arabic speakers who had resisted Egyptian occupation, were defeated and allowed to serve the Egyptian rulers as tax collectors and irregular cavalry under their own shaykhs. The Egyptians divided Sudan into provinces, which they then subdivided into smaller administrative units that usually corresponded to tribal territories. In 1835 Khartoum became the seat of the hakimadar (governor general); many garrison towns also developed into administrative centers in their respective regions. At the local level, shaykhs and traditional tribal chieftains assumed administrative responsibilities. 

In the 1850s, the pashalik revised the legal systems in Egypt and Sudan, introducing a commercial code and a criminal code administered in secular courts. The change reduced the prestige of the qadis (Islamic judges) whose sharia courts were confined to dealing with matters of personal status. Even in this area, the courts lacked credibility in the eyes of Sudanese Muslims because they conducted hearings according to the Ottoman Empire's Hanafi school of law rather than the stricter Maliki school traditional in the area.  The Turkiyah also encouraged a religious orthodoxy favored in the Ottoman Empire. The government undertook a mosque-building program and staffed religious schools and courts with teachers and judges trained at Cairo's Al Azhar University. The government favored the Khatmiyyah, a traditional religious order, because its leaders preached cooperation with the regime. But Sudanese Muslims condemned the official orthodoxy as decadent because it had rejected many popular beliefs and practices. 

Until its gradual suppression in the 1860s, the slave trade was the most profitable undertaking in Sudan and was the focus of Egyptian interests in the country. The government encouraged economic development through state monopolies that had exported slaves, ivory, and gum arabic. In some areas, tribal land, which had been held in common, became the private property of the shaykhs and was sometimes sold to buyers outside the tribe. 

Muhammad Ali's immediate successors, Abbas I (1849-54) and Said (1854-63), lacked leadership qualities and paid little attention to Sudan, but the reign of Ismail (1863-79) revitalized Egyptian interest in the country. In 1865 the Ottoman Empire ceded the Red Sea coast and its ports to Egypt. Two years later, the Ottoman sultan granted Ismail the title of khedive (sovereign prince). Egypt organized and garrisoned the new provinces of Upper Nile, Bahr al Ghazal, and Equatoria and, in 1874, conquered and annexed Darfur. Ismail named Europeans to provincial governorships and appointed Sudanese to more responsible government positions. Under prodding from Britain, Ismail took steps to complete the elimination of the slave trade in the north of present-day Sudan. The khedive also tried to build a new army on the European model that no longer would depend on slaves to provide manpower. However, this modernization process caused unrest. Army units mutinied, and many Sudanese resented the quartering of troops among the civilian population and the use of Sudanese forced labor on public projects. Efforts to suppress the slave trade angered the urban merchant class and the Baqqara Arabs, who had grown prosperous by selling slaves. 

There is little documentation for the history of the southern Sudanese provinces until the introduction of the Turkiyah in the north in the early 1820s and the subsequent extension of slave raiding into the south. Information about their peoples before that time is based largely on oral history. According to these traditions, the Nilotic peoples--the Dinka, Nuer, Shilluk, and others--first entered southern Sudan sometime before the tenth century. During the period from the fifteenth century to the nineteenth century, tribal migrations, largely from the area of Bahr al Ghazal, brought these peoples to their modern locations. Some, like the Shilluk, developed a centralized monarchical tradition that enabled them to preserve their tribal integrity in the face of external pressures in the nineteenth and twentieth centuries. The non-Nilotic Azande people, who entered southern Sudan in the sixteenth century, established the region's largest state. In the eighteenth century, the militaristic Avungara people entered and quickly imposed their authority over the poorly organized and weaker Azande. Avungara power remained largely unchallenged until the arrival of the British at the end of the nineteenth century. Geographic barriers protected the southerners from Islam's advance, enabling them to retain their social and cultural heritage and their political and religious institutions. During the nineteenth century, the slave trade brought southerners into closer contact with Sudanese Arabs and resulted in a deep hatred for the northerners.  Slavery had been an institution of Sudanese life throughout history, but southern Sudan, where slavery flourished particularly, was originally considered an area beyond Cairo's control. Because Sudan had access to Middle East slave markets, the slave trade in the south intensified in the nineteenth century and continued after the British had suppressed slavery in much of sub-Saharan Africa. Annual raids resulted in the capture of countless thousands of southern Sudanese, and the destruction of the region's stability and economy. The horrors associated with the slave trade generated European interest in Sudan. 

Until 1843 Muhammad Ali maintained a state monopoly on slave trading in Egypt and the pashalik. Thereafter, authorities sold licenses to private traders who competed with government- conducted slave raids. In 1854 Cairo ended state participation in the slave trade, and in 1860, in response to European pressure, Egypt prohibited the slave trade. However, the Egyptian army failed to enforce the prohibition against the private armies of the slave traders. The introduction of steamboats and firearms enabled slave traders to overwhelm local resistance and prompted the creation of southern "bush empires" by Baqqara Arabs. 

Ismail implemented a military modernization program and proposed to extend Egyptian rule to the southern region. In 1869 British explorer Sir Samuel Baker received a commission as governor of Equatoria Province, with orders to annex all territory in the White Nile's basin and to suppress the slave trade. In 1874 Charles George Gordon, a British officer, succeeded Baker. Gordon disarmed many slave traders and hanged those who defied him. By the time he became Sudan's governor general in 1877, Gordon had weakened the slave trade in much of the south.