The troops encountered no resistance as they headed towards the city, a senior officer with the Malian army told AFP news agency.
French and Malian troops have been pushing north in their offensive against Islamist rebels.
On Saturday, they seized Gao, the most populous city in northern Mali.
Thousands of people poured out into the streets to celebrate the arrival of the troops.
Islamists seized the north of the country last year, but have been losing ground since French forces launched an operation earlier this month.
The advance comes as African Union leaders are meeting to discuss sending more troops to Mali.
“We control the airport at Timbuktu,” a senior Malian army officer told the AFP.
“We did not encounter any resistance.”
A military spokesman in Paris told the AFP that the French and Malian troops now control access to the city as well as the territory between Timbuktu and Gao.
Once Timbuktu is secured, the French-led troops are expected to focus on the last rebel stronghold, Kidal, near the border with Algeria.
Kidal – home of the head of Ansar Dine, the main militant group in northern Mali – was bombed overnight by French forces, Malian officials say.
Once Kidal is taken, the first phase of the French operation will be over.
The second phase will be to track down the militants to their desert hideouts, which could prove a much more difficult task.
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