Investigators are expected to question the men in France, where the case is likely to draw parallels with Mohammed Merah, the 23-year-old who shot dead seven people in southwest France in March 2012 after returning from Pakistan.
Investigators said Pakistani police arrested the trio on May 28th last year after they entered the country illegally from Iran.
They were detained along with Naamen Meziche, another Frenchman of North African extraction previously known to Western security services as a presumed member of Al-Qaeda.
"They said they came to Pakistan to deepen their knowledge of Islam and to fight in Afghanistan," one investigator told AFP on condition of anonymity.
Meziche's arrest was announced last June but French and Pakistani officials had kept quiet about the other three.
At the time, Pakistani officials said Meziche was probably heading to Somalia.
But Western experts said he had been en route to Pakistan's semi-autonomous tribal belt on the Afghan border, an Al-Qaeda and Taliban stronghold.
Investigators believe Meziche could have been taking the other three to the tribal belt, a rear base for the Taliban's war in Afghanistan and a location of Al-Qaeda training camps.
Officials say the three men left France in January 2012, telling their families in Orléans, south of Paris, that they were going on pilgrimage to Mecca in Saudi Arabia, but five months later they were detained in Pakistan.
On Thursday a French diplomatic source confirmed that the last of the three suspects was now back on French soil, after being deported over the last 48 hours.
Their precise link to Meziche, who will also be deported, remains unclear.
It also remains unclear whether they will face trial. A new law banning French citizens from going abroad for militant training came into force last December, after their arrest.