The protesters clashed with security forces in the capital Cairo and in Dakahlia province on Saturday, condemning the death sentences given to the Brotherhood members.
Earlier in the day, a court had sentenced to death MB’s spiritual leader Mohammed Badie and over 180 others in the latest mass trial following last year's military coup that toppled the country's first democratically-elected president Mohamed Morsi.
The ruling by the southern Minya Criminal Court is the largest confirmed mass death sentence to be handed down in Egypt in recent memory.
It is also the second death sentence for the Brotherhood's Supreme Guide Mohammed Badie since the military-installed government launched the crackdown against MB and its supporters.
In Cairo, meanwhile, the protesters gathered to march to the presidential palace to denounce the country's protest law, which bans unauthorized gatherings and threatens prison and heavy fines for violators.
The protesters however did not make it through to the palace as they came under attack by men in civilian clothes and by police who fired tear gas to disperse them.
"There has been an excess in using the death sentences recently, which will only lead to more violence in society because people are now used to the idea of execution, killing and blood," prominent rights lawyer Negad el-Borai said.
Amnesty International described the ruling as one more "alarming sign of the Egyptian judiciary's increasing politicization," especially with "notable spike" in death sentences.