Qaradawi's International Union of Muslim Scholars described as "criminal and unlawful" an offensive led by the group's fighters against non-Muslims in northern Iraq earlier this month.
The Egyptian-born cleric wields huge influence with the Brotherhood's supporters across the Arab world through his frequent appearances on Al-Jazeera television from his base in exile in Qatar.
His group said it "categorically prohibits the actions of some excessive and deviant groups, such as killing innocent Muslims and non-Muslims, under the cover of repugnant sectarianism one time, or under the name of the so-called Islamic State the other time."
It was the latest in a series of condemnations of the Islamic State by Qaradawi's organisation since the jihadists launched a lightning offensive in Iraq's second city Mosul in early June, swiftly overrunning much of the Sunni Arab heartland north and west of Baghdad.
The group also controls much of eastern Syria, including the whole of the Euphrates Valley province of Raqa and much of Deir Ezzor province downstream.
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A UN-mandated probe charged Wednesday that public executions, amputations, lashings and mock crucifixions have become a regular fixture in areas of Syria controlled by IS.
Qaradawi, who was born in Egypt, has been based in Qatar for decades.
He is seen as a spiritual guide to the Brotherhood of ousted Egyptian president Mohamed Morsi and is wanted by the authorities in Cairo where he faces trial in absentia.
Qatar had close ties with Egypt during Morsi's turbulent single year in power but relations nose-dived after his overthrow in July last year.
The gas-rich Gulf state has given refuge to a number of Brotherhood leaders who fled the bloody crackdown that followed Morsi's ouster.
Egypt has called on Qatar to respect a 1998 Arab counter-terrorism treaty and hand over Qaradawi and other wanted Islamists.