Morsi, 62, will stand trial with 14 other members of his Muslim Brotherhood over the killings of at least 10 protesters outside his presidential palace in December 2012, according to state news agency MENA.
He will stand trial before a Cairo district court. The Cairo Appeals Court named judge Ahmed Sabry Youssef to preside over the trial.
Prosecutors have charged Morsi with "inciting his supporters to commit premeditated murder" during the December 5 clashes.
The clashes broke out between Morsi loyalists and his opponents after he passed a temporary decree placing his decisions above judicial review. Six months later Morsi was ousted by the powerful military.
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Since his July 3 ouster, Morsi has been held by the army in an undisclosed location.
Hundreds of people demanding his reinstatement - mostly Brotherhood supporters - have since been killed in clashes with security forces. More than 50 died at protests held in several cities on Sunday.
His trial is likely to spark more protests from his supporters who demand his release.
Morsi, who became Egypt's first democratically elected president, will be the country's second president standing trial over the killings of protesters.
Morsi is also being investigated over allegations related to his escape from prison during the uprising that forced Hosni Mubarak from power in 2011, including that he conspired with the Palestinian Islamist militant group Hamas, an offshoot of the Brotherhood.
After Morsi's ouster authorities launched a crackdown against the Muslim Brotherhood and its members.
Much of the Brotherhood's leadership, including Supreme Guide Mohamed Badie, are standing trial on other charges.
The Muslim Brotherhood's status as a registered non-governmental organisation was officially annulled yesterday as part of the crackdown.