The pair are just 15-years-old and from the southwestern city of Toulouse. Their families claim they have been brainwashed on the Internet, the New York Daily News reported on Saturday.
One of the boys, known only as Hakim, left a note for his father on January 6 telling him he was off to fight the war against the Syrian government.
The father added that he had received a phone call from his son claiming he was in danger in Syria but would not call again for a month.
"He's been brainwashed on the Internet," his father told French TV channel, BFM.
The news comes as France is increasingly concerned about the number of French nationals joining the fighting in the almost three-year long Syrian conflict.
President Hollande said earlier this week that 700 French people had travelled to Syria to fight, amid fears that many are being radicalized.
Toulouse is also the city where an al-Qaeda inspired gunman Mohamed Merah shot dead seven people two years ago, including three children.
NTJ/HH