The decision to seize the group's assets and close down its St Petersburg head office followed a request from the ministry of justice, which claimed it had found signs of "extremist activity" within the organisation.
Judges ordered the closure of the group's Russian headquarters and 395 local chapters, as well as the seizure of its property. The order makes it illegal for the group to hold meetings or distribute any information about themselves, or any published and printed material. The ban will not come into force until after the group's appeal is heard.
In its lawsuit the Justice Ministry mentioned various violations, exposed by a snap check of the organization's activities, including those of the federal law on resistance to extremist activities.
The religious movement, which has 395 centres across Russian Federation, has vowed to appeal the decision.
Other groups banned in the country are militant organisations al-Qaeda and the Islamic State.
Russian authorities have put several Jehovah's Witness publications on a list of banned extremist literature.
The Justice Ministry began an investigation into the group's practices in February. The Moscow City Court on January 16, 2017 upheld the warning over extremism handed to Jehovah's Witnesses.
Jehovah's Witnesses did not offer an immediate reaction to the ruling, but in a statement following the original declaration it said "extremism is profoundly alien to the Bible-based beliefs and morality" of members of the faith.
Four former members of the Jehovah's Witnesses had told a Russia's Supreme Court how they were brainwashed by the church against receiving higher education or starting a family.