The men received life terms on Tuesday on charges of “shooting and adopting violent means” against the army in the port city of Suez on August 14.
The court handed five-year jail terms to 45 other Brotherhood members while eight defendants were acquitted.
The clashes erupted following a military crackdown in the streets of Cairo against the supporters of ousted president, Mohamed Morsi.
On July 3, the Egyptian Army removed the democratically-elected Morsi from office and declared the head of the Supreme Constitutional Court, Adly Mahmoud Mansour, as the country’s interim president. The army also suspended the constitution and dissolved the parliament.
The army-appointed government has launched a bloody crackdown on Morsi supporters and arrested more than 2,000 Brotherhood members.
On Monday, a judicial advisory panel set up by the country’s military-backed government accused the Brotherhood of operating outside the law.
It also recommended the dissolution of the group, which is a legally registered non-governmental organization (NGO).
The move comes shortly after the arrest of the Brotherhood’s supreme leader, Mohamed Badie, on August 20 on charges of “inciting violence.”
Badie had said the coup against Morsi was illegal and vowed to “complete the revolution” that toppled the Western-backed regime of former Egyptian dictator Hosni Mubarak in 2011.
Nearly 1,000 people were killed in a week of violence between anti-coup protesters and security forces after police dispersed their protest camps in Cairo in a deadly operation on August 14.
The massacre sparked international condemnation and prompted world bodies to call for an independent investigation into the violence.