"Fighters from several Islamist rebel brigades took control of the children's hospital in the Qadi Askar district, which is the headquarters of the Islamic State of Iraq and the Levant in the city," the So-called Syrian Observatory for Human Rights said on Wednesday.
The Observatory said it was unclear what had happened to "hundreds" of ISIL fighters who had been inside the headquarters.
The rebels freed dozens of people who were being held prisoner in the ISIL headquarters, it added, citing initial reports.
ISIL has been fighting a coalition of rivel rebels angered by a spate of abuses by the terrorists, who have been accused of kidnapping and killing civilians and rival rebels.
Late Tuesday, an ISIL spokesman said the group would "crush" opposition fighters and warned that it considered members of the opposition National Coalition and the military command of the so-called Free Syrian Army to be "legitimate targets."
BA/BA