Hundreds of local people had gathered in Timbuktu's main square to thank Hollande for ordering the French intervention that has driven Al-Qaida-linked militias from most of northern Mali.
Earlier he landed at the strategically important airfield at Sévaré, where he was met by Mali's interim President Dioncounda Traoré, who accompanied him to Timbuktu.
Hollande was to meet French and Malian troops to thank them for their role in the offensive, as well as Muslim imams anxious to distance themselves from the fundamentalists.
He was also set to visit a historic mosque and the centre where historic manuscripts, some of which were reported to have been destroyed, are destroyed.
Hollande was accompanied by Foreign Affairs Minister Laurent Fabius, Defence Minister Jean-Yves Le Drian and Development Minister Pascal Canfin.
"Since the beginning of the French military intervention, it has to be said that François Hollande's popularity has exploded here," comments RFI's website in French, adding that some Malians jokingly propose that he become their president.
Hollande and Traoré were scheduled to go to the capital, Bamako, later Saturday to deliver speeches and discuss Mali's future, including proposed elections.
The only point of discord between them is likely to be the French decision to arrive in the northern town of Kidal without even informing the Malians.
Rights groups have reported a number of atrocities during the offensive.