Mursi was charged with inciting the killing of protesters, in connection to the deaths of 10 people outside the presidential palace in December 2012.
He also faces serious charges in three other cases.
Mursi was deposed by his then military chief and Minister of Defence Abdel Fattah el-Sisi after mass protests against his rule in the summer of 2013.
Following the coup, the former president's supporters launched a series of protests and sit-ins across the country culminating in a crackdown by security forces that left hundreds dead.
In the deadliest incident, at least 817 protesters were killed in Cairo's Rabaa al-Adawiya Square when security forces opened fire on a sit-in. Human Rights Watch (HRW) said the killings likely amounted to "crimes against humanity".
Thousands have also been imprisoned, with many supporters of Mursi facing mass trials facing charges of involvement in violence, Al Jazeera reported.
At least 1,212 have been sentenced to death since the start of 2014, including the head of the Muslim Brotherhood, Mohamed Badie.