In another case signalling growing intolerance of dissent by military-backed authorities, a pro-democracy movement that helped ignite the uprising that toppled autocrat Hosni Mubarak in 2011 was banned by court order, judicial sources said.
The death sentence passed on Mohamed Badie, the Brotherhood's general guide, will infuriate members of the group, which has been the target of raids, arrests and bans since the army forced President Mohamed Mursi from power in July.
"If they executed me one thousand times I will not retreat from the right path," Badie was quoted as saying by lawyer Osama Mursi.
The movement says it is committed to peaceful activism. But some Brotherhood members fear pressure from security forces and the courts could drive some young members to violence against the movement's old enemy, the Egyptian state.
Badie was charged with crimes including inciting violence that followed the army overthrow of Mr Mursi, who is also on trial on an array of charges.
In a separate case, the court handed down a final capital punishment ruling for 37 others. The death sentences were part of a final judgement on 529 Muslim Brotherhood supporters sentenced to death last month. The remaining defendants were jailed for life, judicial sources said.
Death sentence recommendations in the case involving Badie will be passed on to Egypt's Mufti, the highest religious authority. His opinion can be ignored by the court.
Mass trials in the biggest Arab state have reinforced fears among human rights groups that the government and anti-Islamist judges are using all levers of power to crush opponents.
"The decisions are possibly the largest possible death sentences in recent world history.
"While they are exceptional in scale, they are certainly not exceptional in kind," said Sarah Leah Whitson, executive director for Middle East and North Africa at Human Rights Watch.
"It seems these sentences are aimed at striking fear and terror into the hearts of those who oppose the interim government."
Meanwhile, the pan-Arab satellite network Al Jazeera served Egypt with an £89million compensation claim for what it said was damage to its business inflicted by Cairo's military rulers, said a lawyer acting for the Qatar-based channel.
He said Egypt had waged a "sustained campaign" against the broadcaster and its journalists since the army toppled Mr Mursi last July.
The lawyer said Cairo had six months to settle the claim, which was filed in the context of a bilateral investment treaty, or face a tribunal.