Al Azhar, which is considered Sunni Islam's oldest seat of learning, described the group as "extremist".
“It is clear to the public what these groups have done in distorting some texts, cutting them out of their context, and using them to achieve personal goals or interests and corrupting the land,” Al Azhar's fatwa centre said in a statement.
“Membership in these extremist groups is considered forbidden by Shariah,” it added, referring to the Islamic laws.
Founded in 1928, the Brotherhood established itself in the mid-20th century as the main opposition movement in Egypt, as well as in other countries in the region.
But the movement was wiped from Egypt's political landscape in 2013, after a brief one-year tenure by one of its members Mohamed Morsi - the first democratically-elected president in Egypt's history.
He was was ousted in a coup by the army in 2013, and since then hundreds of Brotherhood members have faced mass trials relating to alleged violence or incitement.
Morsi, who had been detained since the coup, died during a court hearing in June 2019.
According to rights groups, more than 800 Muslim Brotherhood supporters were killed in a single day in August 2013 during demonstrations in the capital.
Cairo blacklisted the Brotherhood as a "terrorist" organisation in 2013, but the Islamist group has consistently denied any link to violence.
Al Azhar's fatwa on the Brotherhood comes amid what has been described by observers as a sustained assault on the independence of the religious institution by Egypt's government.
The coordinated attack on the Muslim Brotherhood has been widely condemned, including in a statement by global Islamic scholars who called on Riyadh to reconsider its designation.
The group of 18 Muslim scholar associations called for unity among Muslims and said the discourse of scholars should not be politicised, Arabi21 reported in November.
In a joint statement, religious scholar associations from Sudan, Libya, Lebanon, Palestine and other countries backed the Muslim Brotherhood as "defenders" of Islam.
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"The Muslim Brotherhood is a missionary group … including a large number of scholars, preachers and Mujahideen have joined the effort to defend the doctrine of Islam and its Sharia," the associations said.
Talat Fehmi, a spokesperson for the Muslim Brotherhood, told Anadolu Agency that the organisation denies all accusations made by the council.
"The Brotherhood ... is far from violence, terror and tearing apart the ummah. Since its establishment, it has been calling people to Allah with good advice," Fehmi said.