The Court of Cassation ordered that the 65-year-old be retried on the charge of conspiring to commit terrorist acts with foreign organisations.
Last week, the court quashed a death sentence handed to Morsi in a separate case revolving around a mass prison break during the 2011 revolution.
But he is still serving lengthy sentences related to two other cases.
Morsi became Egypt’s first democratically elected president in 2012, but he was removed by the military a year later after mass protests against his rule.
Since then, the authorities have launched a crackdown on Morsi’s now-banned Islamist movement, the Muslim Brotherhood, which has seen hundreds of people killed in clashes with security forces and tens of thousands imprisoned.