Francois Hollande last month ordered French troops into Mali to help fight al-Qaida-linked forces that had taken control of the African country's northern region.
Hundreds of people greeted the French president in Timbuktu's square after he flew into Sevare, where he was met by interim Malian President Dioncounda Traore, Radio France Internationale reported.
Later, he and Traore were to travel to the capital Bamako to discuss Mali's future, but not before Hollande met with French and Malian troops.
While in Timbuktu, the French president was to visit a historic mosque and a center where some historic books, documents and manuscripts had been burned by fleeing militants.
He is joined on the trip by Foreign Affairs Minister Laurent Fabius, Defense Minister Jean-Yves Le Drian and Development Minister Pascal Canfin.
As Hollande toured Timbuktu to cries of "Vive la France," French and Malian troops who captured the airport in Kidal were trying to secure their hold on the city in northeastern Mali that is considered the last stronghold of the Islamic militants, the BBC reported.
On Friday, Human Rights Watch charged that Malian troops had summarily executed 13 people last month suspected of being supporters of the militants and were responsible for the disappearances of five others, CNN reported.
Both French and Malian officials have repeatedly called on their forces to respect international law and human rights.