The former hostages - Pierre Legrand, Daniel Larribe, Thierry Dol and Marc Féret - were captured by Al-Qaeda in the Islamic Maghreb (Aqim) in Niger, where they were working for French nuclear giant Areva.
They took off from Niamey at about 6.00am universal time in a white government plane and were due to arrive at Villacoublay military airport at 10.45am where they will be met by President François Hollande.
The four were in "very good shape", according to Foreign Minister Laurent Fabius, who accompanied them.
They had appeared thin but in good health and had trimmed the thick beards that they had grown during their captivity, according to reporters in Niamey.
Hollande thanked Niger President Mahamadou Issoufou for his role in the release without giving details.
Defence Minister Jean-Yves Le Drian said on Tuesday that there had been no military operation to free the men, nor had a ransom been paid.
Former French secret service anti-terror operative Louis Caproli does not believe the minister.
"I don't see any other possibility apart from the payment of a ransom," he told RFI. "Because, in spite of all the talent of the president of Niger and of the negotiators, I don't see why Aqim would have freed people they have held for three years, just to please France."
Hollande earlier this year announced that France would refuse to pay ransoms for hostages' release.
Larribe's wife, Françoise, a Malagasy and a Togolese national were freed by Aqim in 2011.
At least seven French nationals are still being held hostage around the world.