French army spokesperson Pierre Gaudilliere said the convoy arrived in N'Djamena "without any particular problems" after spending 10 days on the road in coordination with Nigerien forces.
France's forward bases in Ouallam and Ayorou in northwestern Niger , near the borders with Burkina Faso and Mali, had been partially vacated, Gaudilliere added.
Speaking to AFP, a French military source said, the "three borders" zone is known as a haven for the Islamic State group, IS, but the threat level for troops traveling from Niamey to N'Djamena was "low."
France deployed 1,400 soldiers, fighter jets, drones, helicopters and armored vehicles, in Niamey and western Niger to battle fighters linked to IS and al-Qaida.
N'Djamena is the site of France's military headquarters for the whole Sahel region, housing approximately 1,000 troops.
From Chad, some French troops are scheduled to leave by air with their most sensitive equipment, while others will travel by land and sea.
The pullout is expected to be completed by the end of December.
The French military spokesman said some heavy military equipment was expected to be moved by sea, but the route had yet to be decided in talks with local governments.
"When we speak about an orderly retreat, security and cooperation, all these words are important," said the military spokesperson said.
The pullout, ordered by Niger's military rulers, started last week after the July ouster of President Mohamed Bazoum, a key ally of Paris, had thrown France's strategy for the Sahel region into disarray.
It is the third time in 18 months that French troops have been sent packing by a former African colony, dealing a severe blow to France's influence on the continent and prestige on the international stage.
France earlier pulled out troops from Mali and Burkina Faso, which have undergone coups in the past two years.
On Wednesday, French President Emmanuel Macron hosted Chad's President Mahamat Idriss Deby for talks at the Elysee Palace to discuss regional issues and the return of France's "military assets".