By 1890, Europeans had established their claims to all of Africa's coastal land except for Morocco (independent) and Liberia (independent under USA protection). Ethiopia remained independent in the East African interior, as did the two Boer Republics and a few African states in South Africa. The major European powers threatened them all as they continued to stake claims and try to divide up whatever was left of Africa.

The biggest remaining prize was the Congo basin, which received special status at the Congress of Berlin as the "Congo Free State." It was administered by an international association headed by King Leopold II of Belgium, a country whose neutrality was guaranteed by the 1839 treaty that created it. The other major unclaimed region was in the Upper Nile River Valley (modern Sudan and Uganda).

British efforts to reach the Upper Nile Valley began with the expedition to relieve Gordon and his Egyptian garrison at Khartoum in 1885. The effort failed and the Upper Nile Valley remained in a state of rebellion for the next decade. By 1895, all that remained of Egyptian authority in the Upper Nile Valley was a British post on the Red Sea at Suarkin and a garrison in the province of Equatoria, far to the south near Kenya.

Meanwhile, the French remained angry over the British occupation of Egypt in 1882 and its refusal to honor a promise to withdraw once order was restored. In February 1895 a member of the French parliament and leader of the "pro-colonial" faction urged his colleagues to approve an advance towards the Nile from its southern end unless the British withdrew. A month later, a British member of parliament declared that the entire Nile Valley belonged to the British. By the end of the year, the race was on to claim the Upper Nile Valley.

The Italians got a head start from their Eritrean outpost at Massawa on the Red Sea, but their defeat by the Ethiopians at Adowa in March 1896 ended their effort. In September 1896, King Leopold, leader of the Congo Free State, dispatched a huge column of 5000 Congolese troops with artillery towards the White Nile River from Stanleyville on the Upper Congo River. They took five months to reach Lake Albert on the White Nile, about five hundred miles from Fashoda, but by then, their soldiers were so angry at their pace and treatment that they mutinied on March 18, 1897. Many of the Belgian officers were killed, some were eaten, and the rest were forced to flee.

Meanwhile, the French began to assemble their own expedition by sending Captain Jean-Baptiste Marchand to West Africa. By June 20, 1896, he reached Libreville in the colony of Gabon with a force that included eleven French naval officers and 150 Senegalese soldiers.

It took them nearly four months to move about 100 tons of supplies to the navigable portion of the Congo River and six more months to reach Bangui by steamboat. From there, they traveled 450 miles by river and overland to the last French post at Ouango, then dragged their equipment (including a collapsible steel steamboat with a one-ton boiler) overland to the Sué River, a tributary of the Nile. Unfortunately, by the time they reached the Sué, the dry season was underway and it was too shallow to navigate. They had to camp and remain there until the following summer before the water got deep enough to continue.

Eventually, when they got underway again, it took a week to reach the Sudd, an enormous swamp that lay between them and the Nile. It took thirteen more days to cross the swamp, which was inhabited by lethal crocodiles, swarms of mosquitos and Dinka people who warned them not to continue. Eventually, they reached open water on June 25, more than 4000 miles and almost exactly two years from their point of departure on the West African coast. Fifteen days later, they reached Fashoda on July 10, 1898.

While Marchand and his soldiers were waiting for the Sué to rise, a British force led by Lord Kitchener was working its way up the Nile, ostensibly to rescue Italians cut off after the 1896 battle with Ethiopia. Kitchener's force reached Omduran, just north of Khartoum, in September 1898 and defeated a Mahdist army. When he learned of the French presence at Fashoda, he continued upstream by steamboat and arrived at Fashoda on September 19.

The Fashoda Incident showed that Europeans could still avoid open warfare over African territory, something that they would fail to avoid a generation later when World War I broke out. The defeat of the Mahdist forces left a power vacuum in the Upper Nile Valley which the British filled with Egyptian troops (plus British officers) by creating the fiction that Egypt was still independent.

The French were humiliated by their "defeat" at Fashoda, but it had less influence than the loss of French territory to Prussia in 1870, so instead of looking for revenge against the British, the French put aside their grievances, joined a military alliance with the British (the Entente Cordial of 1904), and focused on developing their rather spacious territories in West Africa.