The 2013 law, which has been used to jail activists for up to two years, required demonstrators to inform the interior ministry that they were planning a protest.
The ministry could then refuse permission.
The Supreme Constitutional Court ruled that the article was unconstitutional, said barrister Tareq Shibel.
The court said in a statement that the constitution guaranteed freedom of association and the right to peaceful protest.
The ruling does not however mean the law would be scrapped in its entirety, said two court officials who did not be wish to be named.
A crackdown on Islamist supporters of Morsi after his ouster saw hundreds of demonstrators killed and thousands jailed, including secular dissidents.
Jihadist attacks have since killed hundreds of soldiers and policemen.
The United Nations and rights groups had asked the Egyptian government to reconsider the protest law.
In October Sisi said his government would look into revising the law, shortly after pardoning 82 detainees imprisoned on political grounds or over freedom of expression.
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