It was at his suggestion that the marquis de Chasseloup-Laubat determined to send a mission to explore the valley of the Mekong River, but as Garnier was not considered old enough to be put in command, the chief authority was entrusted to Captain Ernest Doudard de Lagrée. In the course of the expedition - to quote the words of Sir Roderick Murchison addressed to the youthful traveller when, in 1870, he was presented with the Victoria Medal of the Royal Geographical Society of London - "from Kratie in Cambodia to Shanghai 5392 miles were traversed, and of these, 3625 miles, chiefly of country unknown to European geography, were surveyed with care, and the positions fixed by astronomical observations, nearly the whole of the observations being taken by Garnier himself". Volunteering to lead a detachment to Dali, the capital of Sultan Suleiman, the sovereign of the Muslim rebels in Yunnan, Garnier successfully carried out the more-than-adventurous enterprise. When shortly afterwards Lagrée died, Garnier naturally assumed the command of the expedition, and he conducted it in safety to the Yangtze River, and thus to the Chinese coast. On his return to France, he was received with enthusiasm. The preparation of his narrative was interrupted by the Franco-Prussian War, and during the siege of Paris, Garnier served as principal staff officer to the admiral in command of the eighth sector. His experiences during the siege were published anonymously in the feuilleton of Le Temps, and appeared separately as Le Siège de Paris, journal d'un officier de marine (1871).

Returning to Cochinchina, he found the political circumstances of the country unfavourable to further exploration, so accordingly, he went to China, and in 1873 followed the upper course of the Yangtze River to the waterfalls. Garnier met his death in controversial circumstances. In late 1873 he was sent by Admiral Dupré, the governor of Cochinchina, to Tonkin, to resolve a dispute between the Vietnamese authorities and the French entrepreneur Jean Dupuis. Persuaded that the time was ripe for a French conquest of Tonkin, Garnier captured Hanoi, the capital of Tonkin, 20 November 1873. In the next few weeks a small French force under Garnier's command captured most of the citadels of the Red River Delta. The Vietnamese authorities, despairing of meeting the French with their own forces, appealed to the notorious Chinese soldier of fortune Liu Yongfu to come to their aid with his Black Flag Army.

On 21 December 1873 Liu Yongfu and around 600 Black Flags (French: pavillons noirs, drapeaux noirs), marching beneath an enormous black banner, approached the west gate of Hanoi. A large Vietnamese army followed in their wake. Garnier began shelling the Black Flags with a field piece mounted above the gate, and when they began to fall back led a party of 18 French marine infantrymen out of the city to chase them away. The attack failed. Garnier, leading three men uphill in a bayonet attack on a party of Black Flags, was stabbed and hacked to death by several Black Flag soldiers after stumbling in a watercourse. The youthful enseigne de vaisseau Adrien-Paul Balny d’ Avricourt led an equally small column out of the citadel to support Garnier, but was also killed at the head of his men. Three French soldiers were also killed in these sorties, and the others fled back to the citadel after their officers fell. Garnier's death effectively ended the first French adventure in Tonkin. The French government disavowed Garnier's adventure and hastened to conclude a peace settlement with the Vietnamese, abandoning most of its claims in Tonkin.

Garnier's chief fame rests on the fact that he originated the idea of exploring the Mekong, and carried out the larger portion of the work. During the French colonial period he was also honoured for his feats of arms in Tonkin, which paved the way for the eventual French conquest of Tonkin in the 1880s.

In 1883, nine years after Francis Garnier's death, the French naval officer Henri Rivière was also killed by the Black Flags in Tonkin, in remarkably similar circumstances. Garnier and Rivière were honoured during the French colonial period as the two pre-eminent French martyrs of the conquest of Tonkin. In 1884, during the Sino-French War, two gunboats of the Tonkin Flotilla were named after the two men. During the siege of Tuyen Quang (November 1884–March 1885), Liu Yung-fu's Black Flags, who formed part of the besieging Chinese army, taunted the men of the French garrison by chanting the names of their two most famous victims: 'Garnier! Rivière! Garnier! Rivière!'

In 1943, French Indochina issued a postage stamp commemorating Garnier.