Three Turkish F-16s took off from the southeastern Turkish city of Diyarbakir and conducted an early morning bombing raid against three IS targets, dropping four guided bombs, the statement said.
The operation came after the first major cross-border clashes between Turkey and IS jihadists on Thursday that left one Turkish soldier and one militant dead.
The decision to launch the air operation was taken at a meeting of security officials in Ankara late Thursday chaired by Turkish Prime Minister Ahmet Davutoglu.
"In this context.... an operation was carried out against targets belonging to Daesh inside the Syrian border," the statement said, using an Arabic acronym for the group.
"Three of our F-16s hit... three targets belonging to Daesh," it said, adding that "the government of the Turkish Republic is determined to take the necessary measures to protect national security".
The planes dropped their bombs just before 4:00 am local time (0100 GMT) and all returned safely to their base.
The bombing raid was the first such by the Turkish air force on IS since the Islamists began their advance across Iraq and Syria in 2013, seizing control of swathes of territory right up to the Turkish border.
It came after one soldier was killed and two sergeants wounded on Thursday by fire from five IS militants on the Syrian side of the border.
Four Turkish tanks from the fifth armoured brigade responded by opening fire on IS targets in Syria in the most serious cross-border clashes yet between the two sides.
The fighting erupted after the killing of 32 people in a suicide bombing Monday in a Turkish town on the Syrian border, blamed on IS, sparked an upsurge in violence in Turkey's Kurdish-dominated southeast.
It also came as Turkey, after months of negotiations, finally gave the green light for the US to use a key air base in its south for air strikes against IS.
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