Judge Mohamed Nagy Shehata also sentenced to death two Islamists who have fled the country, and handed life terms to 23 detained defendants.
The defendants were accused of plotting unrest from their headquarters in a sprawling Cairo protest camp in the months after the military overthrew Islamist president Mohamed Morsi in July 2013.
Among those sentenced to life in prison was Mohamed Soltan, a US-Egyptian citizen who is on hunger strike.His father Salah Soltan was among the 11 detainees sentenced to death.
The sentencings can be appealed before the Court of Cassation, which has overturned dozens of other death sentences, including against Badie.
So far Egypt has executed one Islamist sentenced to death after Morsi's overthrow, following his conviction of involvement in the murder of a youth during violent protests in July 2013
At a previous session, he had sought the opinion of the country's mufti, the Islamic legal authority, on the death sentences confirmed on Saturday. The mufti has an advisory role under Egyptian law.
Known as the "Rabaa Operations Room" case, the prosecution accused the defendants of organising months of unrest and protests against the ouster of Morsi, a senior Brotherhood figure himself now on trial.
The Rabaa al-Adawiya protest camp in Cairo was dispersed by police on August 14, 2013 in a 12-hour long operation that left hundreds of protesters and about 10 policemen dead.
Mohamed Soltan was shot in the arm during the dispersal, and was arrested days later as police hunted down Islamist activists who had fled the protest camp.
Police moved in to disperse the camp after weeks of failed European and US-brokered negotiations with the Brotherhood, who publicly insisted on Morsi's return.
The Islamist was the country's first freely elected president and he ruled only for a year before the army toppled him, spurred by massive protests demanding his resignation.
President Abdel Fattah al-Sisi, the former army chief who toppled Morsi and then won an election, has pledged to eradicate the Brotherhood.
The government has blacklisted the movement as a terrorist organisation amid a spike in militant attacks that have killed dozens of policemen and soldiers.