They were charged with causing the deaths of two policemen during clashes at Al-Nahda square in Giza in southern Cairo, as well as other counts of attempted murder and vandalism.
Seventeen people were sentenced to life in prison, 223 were given 15 years and another 22 accused were given three years.
The court acquitted 115 others accused in the case.
Al-Nahda square was one of two sites where Mursi supporters gathered in the weeks following his overthrow by the military in July 2013 led by then general and now President Abdel Fattah El-Sisi. Sissi was elected in 2014 and is expected to seek a second term in a March vote this year.
Authorities broke up the two sit-ins — at Al-Nahda and Rabaa squares — in August 2013, killing hundreds of protesters. Protests were banned shortly after the two pro-Mursi camps were dispersed and scores were arrested.
Hundreds of Mursi sympathizers have been detained and prosecuted since his ousting. Egypt has banned the Muslim Brotherhood, deeming it a terrorist organization.
The government accuses the Brotherhood of fomenting an insurgency since Mursi’s removal. Militant attacks have killed hundreds of Egyptians, mostly soldiers and police.
Security forces have killed hundreds and detained thousands of members of the group, which says it is committed to political change through peaceful means only.
The court also ordered on Tuesday that those sentenced be fined a total of nearly 40 million Egyptian pounds ($2.27 million) for damaging public property.