Badie and two of his deputies are facing charges of incitement to murder in the deaths of protesters in June, Ahram Online reported Tuesday.
The judges did not indicate what the conflicts were.
Nine anti-Brotherhood protesters were killed and 91 others were injured when the protesters stormed offices of the organization in Cairo.
Badie, deputy Khairat el-Shater, as well as former president Mohamed Morsi, are facing trials on a variety of charges.
Morsi is due to appear in court in November.