Last month, security forces stormed two Cairo protest camps, sparking clashes in which hundreds of Islamist demonstrators were killed.
The operation drew criticism of the military-installed interim authorities from foreign governments and human rights groups.
The United States said Monday it was seeking further details on the Egyptian court's ruling.
Washington has long argued Morsi's Muslim Brotherhood should be part of the political process.
State Department spokeswoman Jen Psaki said: "A transparent inclusive political process that preserves the rights of all Egyptians to participate and leads back to a civilian lead government is critical to the success of Egypt's political and economic future."
A judicial source told AFP the court ruled that a government committee should be created to manage the Brotherhood's seized assets.
The Cairo court "ruled to ban all activities by the Muslim Brotherhood organisation, the group emanating from it and its non-governmental organisation," MENA reported.
The ruling may be appealed and overturned by a higher court.
The Brotherhood slammed the ban, saying it was part of a sustained campaign against the movement.
"The Muslim Brotherhood is part and parcel of Egyptian society. Corrupt and politically motivated judicial decisions cannot change that," it said on its official Twitter account.
It said it was an organisation that "will always be present on the ground even after it is dissolved, and will continue serving the Egyptian people".
The "junta is trying to silence anyone who opposes them. Dissolution verdict is politically motivated and part of a continuous crackdown," it said.
"Muslim Brotherhood remained and will remain, no matter how fascist regimes try to eliminate them. Dissolution will not affect the organisation," it added.
Formed in 1928, the Muslim Brotherhood was banned for decades before a popular uprising overthrew its arch foe president Hosni Mubarak in 2011.
It swept subsequent parliamentary elections and successfully fielded Morsi in last year's presidential election.
The new military-installed government now accuses the Brotherhood of "terrorism", and police have arrested at least 2,000 Islamists, including nearly all of the movement's top leaders.
In the past three years, the movement set up headquarters in a multi-storey building in Cairo and opened offices across the country for its Freedom and Justice Party.
All of these buildings are likely to be seized under the court order. If upheld, the ruling would also criminalise Brotherhood membership.
A government committee is to manage the confiscated assets until criminal courts deliver their verdicts in cases brought against jailed Brotherhood leaders.
The Muslim Brotherhood "used the pure religion of Islam as a cover for activities that contradict true Islam and violate the law," the court ruled.
The decision further reduces the already remote chances of reconciliation between the interim authorities and the influential movement, which still has a loyal grass-roots base.
"A ban represents a blunt approach in which there is no space for the Brotherhood in political and social life," said Michael Hanna, an Egypt specialist with the New York-based Century Foundation think tank.
Senior Brotherhood members had told AFP the movement was willing to concede its core demand for Morsi's reinstatement, but wanted guarantees its imprisoned members would be released and its leaders would be allowed to operate freely.
But the interim government feels little incentive to make a deal with the Brotherhood that would alter its roadmap for a new constitution and then elections by mid-2014, analysts say.
The government says it is for the courts to decide whether to release the Brotherhood members currently in custody, who face charges including incitement to murder.
More than 100 policemen have been killed in clashes with Morsi's supporters since his overthrow.
Dozens of churches and Christian-owned properties have also been torched by Islamists angry at the support given to the coup by the leadership of the Coptic Church.
Under Morsi, the Brotherhood had tried to legalise its status by registering an NGO in its name.
"There were issues of transparency that needed to be addressed in a legal fashion. It should have been allowed to re-register to clarify it's funding stream," Hanna said.
The Brotherhood registered the NGO amid a court case examining the movement's legality.
But the registration, under a government minister belonging to the movement, was opaque and rushed, Hanna said.