Prime Minister Haider al-Abadi ordered the "painful strike" which targeted "a meeting of IS commanders south of al-Dashisha in Syrian territory," a statement said.
F-16 fighter jets were used in the early morning strike and the raid was "successful," the spokesman of Iraq's security media centre, General Yahya Rasool, told AFP.
The security media centre later published a video showing an explosion in the building apparently targeted by the planes, in the middle of an avenue of trees.
مقطع فيديو يظهر الضربة الجوية التي نفذتها طائرات F16 لاستهداف مقر لقيادات داعش في منطقة الدشيشة داخل الاراضي السورية والتي تم الإعلان عنها اليوم الأحد 6 /5/2018 pic.twitter.com/q7K3Vs7FRa
— IRAQI AIR FORCE (@iqAirForce) May 6, 2018
Dashisha is in a desert region of Syria's Hasakah province, where a US-backed Kurdish-led alliance is fighting the jihadists.
"After receiving information on the target in co-operation with Syria's government and in co-ordination with coalition forces (led by the US), F-16s from the Iraqi air force led strikes against a command post of IS, 10 kilometres from the Iraqi border inside Syria," said General Mohammed al-Askari, an adviser to Iraq's defence ministry.
"This attack took place following a meeting of several Daesh commanders who were planning terrorist operations on Syrian or Iraqi territory," he said, using an Arab acronym for ISIS.
The target "was completely destroyed and all the officials there were killed," he said, without giving a death toll.
Askari also said Iraq hosts a centre that co-ordinates military activity with Iran, Russia and Syria "against ISIS."
"This is not the last strike in Syria. They will continue, in relation to the activities of Daesh."
A week ago, Abadi told the media that Iraq would carry out air strikes against ISIS outside the country's own borders.
On April 19, Iraq said it had carried out an air raid against ISIS in Syria that killed 36 IS fighters, near the town of Hajin in the eastern province of Deir ez-Zor.
Iraq declared victory in December against ISIS, which launched a sweeping offensive in 2014 and at one point controlled a third of the country.
The jihadists still control pockets of desert along the border with Syria.
