Mohamed Badie, the Brotherhood’s supreme guide, has already been sentenced to death and prison terms in other trials.
The court also sentenced 48 defendants to jail terms ranging from three to 15 years, and acquitted 20 others. The authorities have arrested thousands of Brotherhood leaders and members, including Morsi, since his ouster by the army in 2013.
Hundreds have been sentenced to death, although many have appealed and won retrials.
On Monday, the court convicted Badie and the other defendants of involvement in clashes in the Suez Canal city of Ismailiya that killed three people.
The country was rocked by violence for weeks after Morsi’s supporters set up protest camps and demonstrated against his overthrow.
The police killed hundreds of his supporters in clashes, including more than 600 on August 14, 2013 as they dispersed a Cairo protest camp.
Morsi, a senior Brotherhood leader, had won the country’s first free election in 2012, more than a year after a popular uprising ousted veteran strongman Hosni Mubarak.
His rule was divisive and millions held protests in Cairo demanding his resignation, prompting the army to overthrow and detain him.