F-16 fighter jets destroyed three houses on Friday which were connected by a trench in the town of Hajin, where the leaders were meeting.
Those killed included high profile targets such as the group's "deputy war minister", one of its "media emirs", its leader Abu Bakr al-Baghdadi's personal courier and its chief of police, the military said in a statement.
Islamic State, which once occupied a third of Iraq's territory, has been largely defeated in the country but still poses a threat along the border with Syria.
"Iraqi F-16 jets carried out a successful air strike that targeted a meeting of Daesh leaders ... in the Hajin area within Syrian territory. The operation resulted in the complete destruction of the targets, and the killing of around 45 terrorists," the military's Joint Operations Command said.
Daesh is an Arabic acronym for Islamic State.
The Iraqi military has carried out several air strikes against Islamic State in Syria since last year, with the approval of the Syrian government of President Bashar al-Assad and the US-led coalition fighting the militants.
Separately, Iran's Revolutionary Guards said one of its senior officers was killed in the Syrian town of Albu Ahmed near the Iraqi border.
Second Brigadier General Shahrokh Daeipour, a veteran of the Iran-Iraq war in the 1980s, was killed during "advisory operations", the Guards' website Sepahnews said, without giving further details.
Iran denies having any conventional armed forces in Syria, but has acknowledged military advisers and volunteers from the Revolutionary Guards are there to help Assad's forces.
Iraq has good relations with Iran and Russia, Assad's main backers in the Syrian war, and also enjoys strong support from the US-led coalition.
Prime Minister Haider al-Abadi declared final victory over Islamic State in December but it still operates from pockets along the border with Syria and has continued to carry out ambushes, assassinations and bombings across Iraq.
The group has resorted to guerrilla tactics since it abandoned its goal of holding territory and creating a self-sufficient caliphate that straddles Iraq and Syria.