The Shilluk constituted the largest component of the Northern Luo group, alongside the Luo of Bahr al-Ghazal and the Anywa near the Sudan–Ethiopia border. They initially settled near Malakal in the early sixteenth century after driving out the Fundj who occupied the confluence of the Nile and Sobat. This position controlled access to Lake No and gave the emerging polity considerable strategic importance.

The Shilluk incorporated Fundj, Nuba, and other elements whose different cultural and economic traditions were combined into what became the Shilluk nation from the second half of the seventeenth century. During this formative period, they developed a mixed economy based on cattle-herding and cereal agriculture. They were essentially sedentary rather than transhumant, living in a chain of villages along the western bank of the Nile between Muomo and Tonga.

By the beginning of the seventeenth century, population pressure on the west bank of the Nile encouraged expansion into two frontier areas. Northward, the Shilluk sought control of the White Nile valley between Muomo and Alays, a region unsuitable for agriculture but rich in game, fish, and honey. From the reign of Odak Ocollo, dated approximately 1600–1635, until 1861, they dominated this area, known to Muslim peoples as Bahr Scheluk.

The Shilluk also contested the region between the Nile and the Nuba Mountains. Their traditions describe support for Darfur in its struggle with the Fundj sultanate over White Nile trade. Later, the arrival of the Jieng in southern Fundj from about 1630 altered the regional balance. The Shilluk and Fundj joined forces to block Jieng expansion northward and westward, pushing it toward the Ethiopian border.

These alliances created a pattern of socio-economic interdependence with Fundj, Djalläba, Bakkära Arabs, Arab freebooters, European traders, and Mahdists. The partnerships were generally formed to exploit or contain the Jieng and were not based on a fixed racial or ethnic ideology. This shifting diplomacy connected military action with trade, frontier control, and access to resources.

Political institutions changed significantly during the second half of the seventeenth century. A sense of national unity developed despite the diversity of the population, and administration became more centralized under the king, or reth. The monarchy gradually established a royal monopoly over economic resources and both local and long-distance trade.

Reth Dhokoth, who reigned approximately from 1670, became known for raids down the Nile and westward into the Nuba Mountains. The famine of 1684 probably encouraged many Shilluk to move northward to raid or settle in Bahr Scheluk, and Dhokoth’s campaigns brought back many captives. His son Togo, associated with the period around 1690–1710, completed much of the centralization, founded Fashoda as the permanent residence of the reth, and instituted an elaborate royal installation ceremony.

Shilluk power expanded as the Fundj empire disintegrated during the eighteenth century. By the end of that century, the Shilluk controlled the White Nile and provided a ferry at Alays for caravan traders travelling between Sennär and al-'Obeyd. Under Reth Nyakwaa, approximately 1780–1820, the Jieng migrated across the Sobat. After Muhammad 'Ali Pasha’s armies invaded Sudan and established Turco-Egyptian rule, Shilluk resistance continued, but from 1821 the frontier retreated southward. A government shipyard at Mandjara, established in 1826, ended Shilluk naval supremacy on the White Nile.