The decision follows the designation of the Brotherhood as a "terrorist organisation" in December, after the military overthrew Islamist president Mohamed Morsi.
The FJP came out on top in every election in Egypt between its creation in the wake of the country's Arab Spring uprising in 2011 and Morsi's removal in July 2013.
The Supreme Administrative Court, in its ruling on Saturday, ordered "the dissolution of the Freedom and Justice Party because it broke the law regarding political parties".
"The party and the Muslim Brotherhood are the same thing" and "its members have committed deeds of violence and acts or terror against the nation", state news agency MENA quoted the prosecution case as stating.
According to media reports, the decision is final and not open to appeal.
The military toppled Morsi, Egypt's first democratically elected president, after massive protests calling for his removal following a single year of turbulent rule.
Since then, a crackdown by the military-installed authorities on his supporters has killed 1400 people in street clashes, and some 16,000 Islamists and protesters have been jailed.
At least 200 people have been sentenced to death in speedy mass trials, including Brotherhood leader Mohamed Badie, although none of the sentences has been carried out so far.
The United Nations has condemned the crackdown as "unprecedented in the recent history" of the world.
