"We hit a training base for Daesh in the west of Iraq," said Marc Gander, communications advisor to Vice-Admiral Eric Chaperon, commander of the warship's battle group.
He used an Arabic acronym to refer to the Islamic State jihadist group.
The target was "close to the borders with Syria, at Abu Qaim," said Gander.
One of the four Rafale fighter jets that took off on Wednesday morning returned having released all four of its guided missiles while another dropped two, an AFP photographer said.
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The two pilots shook hands after stepping down from their planes.
French warplanes have formed part of the US-led coalition carrying out raids against IS jihadists in Iraq for several months.
But the Charles de Gaulle only began operations against the Islamic State group in Iraq on Monday, stepping up France's campaign seven weeks after deadly jihadist attacks in Paris.
The carrier's 12 Rafale jets and nine Super Etendard add to France's nine Rafales based in the United Arab Emirates and six Mirage 2000Ds flying out of Jordan.
The carrier will be operational in the Gulf for eight weeks.