Kousséri was part of the Bornu Empire. In March 1846 Omar (son of Sheik Mohammed), nominal general of the Bornu sultan Ibrahim suffered a defeat at Kousséri.
In 1900 the village was occupied by soldiers of Rabij az-Zubayr (Rabih), a Sudanese warlord. On 3 March it was taken by the combined forces of two French expeditions, one under Major Lamy from Algeria and the other under Lt. Paul Joalland from Senegal and local forces opposed to Rabih. Rabih was not in Kousseri at the time but established himself in a fort on the right bank of the Chari. Lamy did not think he had sufficient forces to attack Rabih immediately, but waited until the beginning of April when he was joined by a third expedition that was coming up the Chari under Emile Gentil. When he arrived the combined forces crossed the Chari and attacked Rabih. The battle of Kousséri was a decisive battle which secured French rule over Chad.