"Two air force Mirage 2000s were engaged in the mission," the defence ministry said. "Simultaneously four Rafale Marines from the aircraft carrier joined them over Syria."
The ministry added that the jets targeted a site yesterday in the northern town of Raqa, the jihadist group's de facto Syrian capital.
France launched its first air strikes from the aircraft carrier earlier yesterday, targeting IS in Iraq.
The Syria air raids happened at 1830 GMT and "destroyed an active site occupied by terrorist fighters in Raqa," the ministry said.
The action came 10 days after coordinated attacks in Paris which left 130 people dead and for which Islamic State has claimed responsibility.
France has ramped up its fight against IS since the attacks and its planes have carried out a number of raids on Raqa from bases in Jordan and the United Arab Emirates in recent days.
The 26 jet fighters on the Charles de Gaulle aircraft carrier triple France's capacity to carry out strikes in the region.
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