French Foreign Minister Catherine Colonna met Sylvain Itté on Wednesday (Sep. 27) "to thank him and his teams for his work in the service of our country under difficult conditions," the ministry said in a written statement to AFP.
The return of the ambassador comes two months after a coup in Niger ousted its president Mohamed Bazoum and prompted a souring in relations between France and its former colony, with Niger's new rulers demanding his departure.
Itté left Niamey with six colleagues "around 4:00 am" (0300 GMT), a diplomatic source had earlier told AFP.
On Sunday (Sep. 24), French President Emmanuel Macron had announced in a TV interview that the ambassador would leave "in the coming hours".
Niger's military leaders -- who overthrew the democratically elected president Mohamed Bazoum on July 26 -- welcomed the announcement.
Born in the Malian capital Bamako in 1959, Itte had been in the post as ambassador to Niger for a year.
His diplomatic career spans 35 years and he was previously ambassador to Uruguay and Angola.
The Junta had told Itte to leave the country after they overthrew Bazoum and took away the envoy's diplomatic immunity and visa.
But a 48-hour ultimatum for him to go, issued in August, passed with him still in place, as the French government refused to comply or to recognise the military regime as legitimate.
Paris had said that only Bazoum's deposed government could order the envoy out.
Macron also announced in his Sunday TV interview that French troops would withdraw from Niger in "the months and weeks to come" with a full pullout "by the end of the year" -- another demand of the Niger regime.
The French president, who had sought to make a special ally of Niger, said military cooperation was "over".
France keeps about 1,500 soldiers in its former West African colony as part of an anti-jihadist deployment in the Sahel.
The coup against Bazoum was the third such putsch in the region in as many years, following similar actions in fellow former French colonies Mali and Burkina Faso in 2021 and 2022, respectively.
The earlier coups also forced the pullouts of French troops.
Niger, like Burkina Faso and Mali, has been targeted by jihadist attacks for several years.
In recent weeks, tens of thousands of people have joined demonstrations and gatherings in Niamey calling for the withdrawal of the French troops from the country.
The United States, which has some 1,100 military personnel in Niger, has said it will "evaluate" its future steps on the crisis following France's announcement.