The fighters’ heads were decapitated during France’s conquest of the North African country, and were transported to the European country as war trophies.
The return of the skulls to Algeria comes amid calls to reexamine the legacy of colonialism.
United Nations human rights chief Michelle Bachelet has urged countries to make amends for “centuries of violence and discrimination”.
This comes following weeks of anti-racial protests worldwide following the death of George Floyd, an unarmed black American killed by police in Minneapolis.
AFP reports the skulls were flown into Algiers airport from France on a Hercules C-130 transport plane, escorted on arrival by Algerian fighter jets.
The remains were received by President Abdelmadjid Tebboune, with the military giving them a guard of honor and a 21-gun salute to highlight their hero status.
The coffins carrying the remains will be taken to the Palace of Culture in Algiers where they will be on display Saturday for the public to pay their respects.
The arrival of the skulls comes just two days before the North African country celebrates its 58th independence anniversary.
After the ceremony on Sunday, the remains will be laid to rest in the martyrs’ section of the capital’s El Alia cemetery, local media reported.
The French presidency, in a statement to AFP, said the return of the remains was a gesture of “friendship” as part of efforts to “reconcile the memories of the French and Algerian people”.
Announcing the repatriations on Thursday, Tebboune said the decapitated fighters “had been deprived of their natural and human right to be buried for more than 170 years”.