Badie had been on the run as the interim government in Egypt tries to crack down on protests at the ousting of President Mohammed Morsi, who has ties to the Brotherhood.
Over 900 Egyptians have died in the violent clashes between the military government and Morsi's Islamist supporters, including Badie's son. Ammar Badie was fatally shot during protests in the capital's Ramses Square.
The administration has declared a nationwide state of emergency and a nighttime curfew.
President Obama has scrapped joint U.S.-Egypt military exercises scheduled for next month in response to the crackdown. The White House announced Monday that it is reviewing the $1.3 billion in military aid provided to Egypt given the violence.