Hoping to cut off the British Cape to Cairo route, the French Government signed orders on February 24, 1896 instructing Captain Marchand to lead an expedition to the Upper Nile and occupy Fashoda. The Marchand Mission, seven French officers and a force of 120 Senegalese tirailleurs, landed at Fashoda on July 10, 1898 and raised the French flag.

On September 2, 1898, British General Kitchener opened the Sudan by defeating the Mahdists at the battle of Omderman. Having learned of the occupation of Fashoda from a captured band of Mahdists, Kitchener set out with five steamers carrying British and Sudanese soldiers. On September 19, Kitchener and his troops landed at Fashoda, where he met Captain Marchand. Kitchener protested the French occupation, claiming Fashoda for Britain by right of conquest (i.e., the victory at Omdurman), while Marchand maintained that the area belonged to France by virtue of the presence of French troops. When Marchand refused to leave, Kitchener raised the Egyptian flag alongside the French in keeping with Britain's "two flags" policy.

France expressed a desire to negotiate spheres of influence in Africa, but Britain refused to enter into negotiations until Marchand and his troops had evacuated Fashoda. On October 17, both the French and the British began shows of strength in strategic areas.

Eventually realizing the hopelessness of the situation, France agreed to remove her troops, and, on December 4, 1898, ordered the evacuation of Fashoda. On March 21, 1899 a convention was signed with France renouncing all claims to Fashoda.