But it sentenced to death 10 defendants who are on the run, and a final ruling on their cases is expected the same day once they are reviewed.
After the army ousted Islamist Mohamed Morsi last July, Badie was one of thousands of the deposed president's supporters arrested in a crackdown that also left more than 1,400 dead.
He is being tried in nearly 40 cases, all of which potentially carry the death penalty, and has already been sentenced to die in one case.
Death sentences in Egypt are referred to the country's top Islamic scholar for an advisory opinion before being ratified. A court may choose to commute the sentences, which can later be challenged in an appeals court.
Defendants tried in absentia also get an automatic retrial if they are ever arrested.
In today's case, Badie is accused of inciting violence in which two people were killed in the Nile Delta city of Qaliub, only days after the military ousted Morsi on July 3.
Today's hearing was raucous, with the 38 defendants in custody, including Badie, chanting anti-military slogans as soon as they entered the dock.
Defence lawyer Ali Kamal said the death sentences "were expected, given the general climate that (encourages) abuses against the defendants."
"The prosecution do not provide evidence but the judiciary continues to issue strong rulings", he added.
Other defendants include senior Brotherhood official Mohamed al-Beltagui, well-known preacher Safwat Hegazy, two former Morsi cabinet ministers and two ex-MPs from the Brotherhood.
Sisi, who led Morsi's ouster, was elected president last week and is expected to be sworn in tomorrow.
Along with Morsi, Badie, Beltagui and Hegazy are being tried on separate charges of mass prison breaks and attacks on police during the 2011 uprising that toppled strongman Hosni Mubarak.
Morsi is due in a separate court in that case today.
He also faces charges of espionage in collaboration with the Palestinian Islamist movement Hamas, and is on trial for inciting the killing of opposition protesters in December 2012 outside the presidential palace.
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