The Frenchman has been identified by media as Michael Dos Santos, 22, an Islamic convert from an eastern Paris suburb.
Earlier, the government identified the first French militant as Maxime Hauchard, a convert from Normandy.
About 1,000 French jihadists are thought to have gone to Syria and Iraq.
France’s PM Manuel Valls said after a security meeting in Beauvais, north of Paris, that “close to 50” French citizens had died in Syria.
“Sadly, we are not surprised to learn that French citizens or residents of France are found at the heart of these cells and taking part in this barbarity,” he added.
On a visit to Australia, President Francois Hollande told reporters in Canberra “there were two French people” in the video.
“One has been categorically identified and the other one is in the process of being identified,” he said.
An official in the Paris prosecutor’s office, Agnes Thibault-Lecuivre, said there was a “strong presumption” that it was Michael Dos Santos, from the Parisian suburb of Champigny-sur-Marne, in the video, AP news agency reports.
According to France 2, Michael Dos Santos had been identified by a friend, who recalled how the man had surprised his family when he suddenly converted to Islam.
Francois Hollande said officials had not established the “exact role” of the two militants.
He called for families to be given more information about the danger of jihadist websites and urged families to be “vigilant” in stopping young people from being recruited by extremists.
Earlier this week, Maxime Hauchard was named by a French prosecutor as one of those leading Syrian prisoners to their execution.
In the latest ISIS video – unlike previous ones showing beheadings – several militants appear with their heads uncovered.
The footage showed 18 Syrian prisoners, described as soldiers, forced to kneel in front of the militants before being beheaded.
The men were described as pilots and officers loyal to Syrian President Bashar al-Assad, Reuters news agency reported.
The video also shows the severed head of Abdul-Rahman Kassig, a US aid worker who was kidnapped in Syria last year.
ISIS said the video was shot in the Syrian town of Dabiq, which features in Islamic prophecies as the site of a final battle between Muslims and their enemies.
Analysts say the video was elaborately produced, but also reflected IS’s weakness, as its militants had been driven off key sites by US-led coalition air strikes.
Concerns about the involvement of French citizens in the conflict were heightened after a gun attack earlier this year on a Jewish museum in Brussels.
The attack, in which four people were killed, was carried out by 29-year-old Mehdi Nemmouche, a Frenchman who had fought as a jihadist in Syria.
France has the largest Muslim community in western Europe outside Russia, and is thought to provide the biggest contingent of Western jihadists in Syria and Iraq.
Earlier this month, France convicted its first such returnee with a jail term of seven years, our correspondent adds.
The government has also given police new powers to confiscate passports, to prevent people travelling abroad to join militants.
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