Following a closed-door hearing on Thursday, the court ruled on a petition from the justice ministry to designate what it called "the Memorial international civic movement" as extremist and ban its activities in Russia.
Memorial said in a statement that there was no such entity but that the ruling still "would allow the authorities to crack down on any Memorial projects, their participants and supporters".
Memorial is one of the oldest and the most renowned Russian human rights organisations.
It was awarded the 2022 Nobel Peace Prize, less than a year after Moscow launched its full-scale invasion of Ukraine, alongside Belarusian activist Ales Bialiatski, who was imprisoned at the time, and the Ukrainian organisation Centre for Civil Liberties.
In a statement on Wednesday, the Norwegian Nobel Committee condemned the actions against the group, calling them "an affront to the fundamental values of human dignity and freedom of expression" and urged Russia to "cease all harassment of Memorial and its members".
Memorial was founded in the late 1980s to ensure that the victims of the Soviet Union's political repression would be remembered, and grew to a network of smaller organisations both in Russia and abroad.
The group had been declared a "foreign agent", a designation that brought additional government scrutiny and carried strong pejorative connotations, and over the years was ordered to pay massive fines for alleged violations of the "foreign agent" law.
Russian courts ordered its two main entities - the human rights centre and the International Memorial - to shut down in December 2021.
Undeterred, the group continued to operate.
In 2023, its members founded an international Memorial association in Geneva.
Earlier in 2026, that association was banned in Russia as undesirable, a label that exposes anyone involved with it to prosecution.
An extremist designation puts even more pressure on the group, as involvement with extremist activities is a criminal offence in Russia punishable by long prison terms.
