Malakal is the city of the Nile. Capital of Upper Nile State, set on the bank of the White Nile some 650 kilometres north of Juba and just above the point where the Sobat River pours in its waters, for a century it was the great river port of southern Sudan: the place where the steamer coming down from Khartoum and the one coming up from the heart of the Sudd crossed paths, loaded and unloaded. In practice, it was the northern gateway to the south.
It is also the heart of a very ancient human geography. Around Malakal live the Shilluk, who call themselves Collo, whose kingdom, founded according to tradition in the second half of the 15th century and ruled by a divine king called the reth, was the most centralised political structure on the upper Nile. Its historical capital, Fashoda (today Kodok), lies a short way downstream and gave its name to one of the most famous diplomatic incidents of the 19th century, when in 1898 France and the United Kingdom came close to war over this stretch of river. To the east and south lies Nuer country.
And it is, put bluntly, one of the hardest-hit cities in Africa so far this century. Between 2013 and 2015 it changed hands twelve times during South Sudan's civil war and was left devastated; since then it has hosted one of the country's largest settlements of internally displaced people, which until February 2026 was the last UN-run Protection of Civilians site in South Sudan. This guide tells the story of Malakal, its place in the story of the Nile and its present, with the restraint the subject demands. It is not a travel guide: every relevant foreign ministry advises against travelling here.
Malakal occupies a strategic point on the White Nile, just downstream of its confluence with the Sobat, in the heart of the territory of the Shilluk kingdom, whose historical capital, Fashoda (today Kodok), lies a short way downstream. In September 1898 that stretch of river was the scene of the Fashoda Incident, the stand-off between Jean-Baptiste Marchand's French expedition and Herbert Kitchener's Anglo-Egyptian forces that brought France and the United Kingdom to the brink of war and ended with the French withdrawal: the episode that sealed British control over the Nile valley. Under the Anglo-Egyptian Condominium (1899-1956), Malakal grew into a garrison and administrative centre, and its modern urban growth is documented above all from 1908. In the 20th century it was the river port and trading hub of the northern part of southern Sudan, and it was caught up in both civil wars. After South Sudan's independence in 2011 it became the capital of Upper Nile and the centre of the oil region; the civil war that began in December 2013 destroyed it almost completely and turned it into one of the country's major centres of displacement.
Read the full history ↓The largest wetland in the Nile basin and the river towns around it: the unfinished Jonglei Canal, Malakal and the Shilluk kingdom, and Bor, where the second war began.
Read the history of The Sudd and the northern Nile →No exact prices: a scale from $ (budget) to $$$$$ (luxury), with 2-3 options per category.
Origins, formation and what the sources say.
Long before Malakal existed, this bank of the White Nile was the heart of one of Africa's most unusual political structures: the Shilluk kingdom. The Shilluk, who call themselves Collo, are a Nilotic people who settled along the river's western bank in an almost unique linear pattern: hundreds of villages lined up kilometre after kilometre along the water, each with its own chief, all under a single ritual authority.
Tradition credits the kingdom's founding to Nyikang, a figure said to have lived in the second half of the 15th century. The ruler, called the reth, was not a king in the European sense but a divine king. He was seen as the living vessel of Nyikang's spirit, and his physical health was believed to be mystically bound to the prosperity of the whole nation. That idea of power made the Shilluk kingdom a classic case study in 20th-century political anthropology.
Around 1690-1710, the reth Tugø, son of Dhøköödhø, made Fashoda the permanent residence of the kings and set up the elaborate investiture ritual that would last for centuries. Fashoda, now Kodok, lies on the western bank of the Nile, a short way downstream from where Malakal would later grow, and it is still the ceremonial centre of the Collo people.
Upstream and to the east, the human landscape changes: this is Nuer territory, and further south, Dinka. The three peoples share a herding and fishing economy tied to the water cycle of the Sudd (flood, retreat, cattle moving down to the toic grasslands) and a history of living side by side, trading and fighting that no modern border has changed.
The city's name comes from that root. Various local accounts trace it to a Collo expression, «Mal-ba-Kal», which shrank to its current form over time. Malakal is quite literally surrounded by Shilluk villages.
In the colonial carve-up of Africa, few things mattered as much as the Nile. Whoever controlled its course controlled Egypt, and whoever controlled Egypt controlled the Suez Canal and the route to India. In the 1890s, France came up with a bold move: send an expedition from the French Congo across central Africa to plant a flag on the White Nile and force London into negotiations.
The expedition was led by Captain Jean-Baptiste Marchand, who crossed the continent with a small column and reached Fashoda, a short distance from present-day Malakal, in July 1898. At almost the same time, to the north, Herbert Kitchener's Anglo-Egyptian army was completing the reconquest of Sudan by defeating the Mahdist State at the Battle of Omdurman in September that year, and was heading up the river.
The two sides met on 19 September 1898. Kitchener, with a far larger force, demanded a withdrawal. Marchand, under orders to hold his ground, refused to move without instructions from Paris. No one fired a shot. For weeks, the two most powerful European powers of the day stood on the brink of war over a handful of mud houses on the White Nile. In November 1898, France ordered the withdrawal.
The Fashoda Incident sealed British control over the Nile valley and, ironically, cleared the way for the Entente Cordiale of 1904 between France and the United Kingdom. For the Shilluk, the episode meant something else: their ritual capital became Kodok on official maps, and their kingdom was absorbed into the administration of the Anglo-Egyptian Condominium.
And for this bank of the Nile it meant, above all, the arrival of the state. Anglo-Egyptian Sudan was established in 1899, and with it came the need for an administrative post and a garrison on the upper Nile. That post would become Malakal.
Malakal as a city is a 20th-century creation. Under the Anglo-Egyptian Condominium (1899-1956), the settlement on the Nile, downstream from where the Sobat joins it, became a garrison for British troops and gradually the administrative centre of Upper Nile Province. One local study dates the city's modern urban growth to between 1908 and 1955.
The river was the reason it existed. In a region without roads, with a vast swamp to the south and a floodplain on either side, the Nile was the only transport infrastructure there was. Malakal was the great halfway port: the place where steamers coming down from Khartoum and those coming up from the Sudd met, loaded and unloaded. Cattle, sorghum, dried fish, cotton, imported goods and passengers all passed through here.
Being a port gave the city a mixed, commercial character that set it apart from the rest of the south. Northern Sudanese, Greek, Syrian-Lebanese, Ethiopian and Eritrean traders lived alongside Shilluk, Nuer and Dinka. The city's food, architecture and language, with far more Arabic than in the deep south, reflect its role as a hinge between two worlds.
The population figures tell the story of its growth: about 33,750 inhabitants in 1983, about 139,450 in 2010, and an estimated 147,450 in 2014. The University of Upper Nile was founded in 1991. It is one of the oldest higher education institutions in what is now South Sudan and a symbol of Malakal's role as a regional capital.
That rise, however, took place between wars. The First Sudanese Civil War (1955-1972) and the Second (1983-2005) swept across the whole region, and Malakal, as provincial capital, port and garrison, was a military target in both. The city grew used to emptying and filling up again.
The discovery of oil in southern Sudan, in Unity and Upper Nile states, changed the strategic weight of the region and of Malakal. The city became a logistics hub for the industry and a knot of interests reaching far beyond the local: southern crude left (and still leaves) by pipeline for Port Sudan on the Red Sea, tying the two Sudans together in an awkward mutual dependence.
The Comprehensive Peace Agreement of January 2005 ended the second civil war and opened a six-year period of autonomy. On 9 July 2011, after an overwhelming referendum, South Sudan became independent and the youngest country in the world. Malakal remained the capital of Upper Nile State and one of the new country's most important cities: a port, a university, an international airport, an administrative centre and the capital of an oil-producing region.
Those were two years of huge expectations. People talked about rebuilding the port, restoring navigation on the Nile between Juba and Khartoum, infrastructure and investment. The city took in returnees coming back from the north after decades of exile, and international organisations opened offices.
On 15 December 2013, a clash within the presidential guard in Juba set off a political crisis that within days turned into civil war, with an ethnic dimension that spread across the whole country. Malakal, with its mix of peoples and its strategic value, was in the worst possible place.
What happened in Malakal between 2013 and 2016 has few modern parallels. Available records show that by October 2015 the city had changed hands twelve times since the war broke out, in successive battles between government and opposition forces, and that it had been destroyed. Each change of control brought looting, burning and displacement. The city's infrastructure (market, hospital, schools, government buildings) was wholly or partly razed again and again.
The population did the only thing it could: flee. Tens of thousands of civilians sheltered inside the perimeter of the base of the United Nations Mission in South Sudan (UNMISS). Faced with a situation without precedent in its peacekeeping history, the UN ended up formalising these perimeters as Protection of Civilians sites: military bases turned into permanent refuge camps inside the country itself. Others fled to villages in the interior, to islands in the Sudd, or across the border into Sudan.
The Malakal site became the largest and the most complex, because of the mix of communities it sheltered (Shilluk, Nuer, Dinka) and because the tensions burning outside were mirrored within it. On 8 June 2023, for example, clashes inside the camp between Nuer and Shilluk groups left at least thirteen civilians dead and around twenty wounded, according to reports at the time. The figure is given here with its source and without adjectives: it is a fact, not an anecdote.
The revitalised peace agreement signed in September 2018 stopped most of the fighting but did not solve the situation of displaced people. As security improved somewhat, the UN began gradually handing the Protection of Civilians sites over to state management and protection, turning them into conventional camps for internally displaced people. Humanitarian organisations warned publicly at the time that conditions in Malakal were not ready for that step.
The displacement figures show the scale. As of September 2024, displacement tracking records counted 89,434 displaced people in Malakal (almost fifteen thousand more than a year earlier) and 17,056 returnees. On food security, the Integrated Food Security Phase Classification (IPC) projected emergency levels, Phase 4, for the area from November 2024 until at least July 2025.
On 13 February 2026, the United Nations Mission in South Sudan handed responsibility for the Malakal Protection of Civilians site to the Upper Nile State authorities. It was the last site still under UN care in the country. Around 40,000 people lived there, moving freely between the settlement and the city. The acting Deputy Special Representative of the Secretary-General, Graham Maitland, set out the principle with bureaucratic precision: the Government is the primary guarantor of the protection of civilians, and UNMISS steps in only when civilians are under threat of physical violence and there are no viable protection alternatives.
It is the end of an era. The Protection of Civilians sites were a historic improvisation (UN military bases turned into towns) that lasted more than a decade and at their peak sheltered hundreds of thousands of people. Their disappearance doesn't mean displacement is over. It means it has a new administrator.
The national picture gives little reason for optimism. The 2018 revitalised agreement was never fully implemented, and in March 2025 the house arrest of First Vice President Riek Machar, after clashes in Nasir, in this same Upper Nile State, and on the outskirts of the capital, left the process at its most fragile point, according to the agreement's own monitors. On top of that comes the war that broke out in Sudan in April 2023. It reversed migration flows across the northern border and pushed hundreds of thousands of people south, many of them along the route through Renk and Malakal.
Foreign ministries are responding accordingly. Spain's Ministry of Foreign Affairs specifically names Unity, Upper Nile and Jonglei as the highest-risk states in the country. The US State Department keeps South Sudan at Level 4 “Do Not Travel”. The British FCDO advises against all travel to the whole country.
And yet Malakal is still Malakal: the port of the White Nile, the gateway out of the Sudd, the city of the Shilluk and the Nuer, the capital of a province that for a century was the hinge between south and north. Its market has been rebuilt more than once. Its university still exists. The river still flows past. Telling its story accurately, including the hard parts, with sources and without embellishment, is the least we owe a city that was destroyed twelve times and is still standing.
