The court declared Jehovah's Witnesses an extremist organization and banned its 175,000 adherents from congregating on Russian territory.
Jehovah's Witnesses said it would appeal the decision.
The Russian government filed suit on March 16 to outlaw the organization, which was already considered an extremist group in St. Petersburg.
Human Rights Watch criticized the decision as "a serious breach of Russia's obligations to respect and protect religious freedom."
"Jehovah's Witnesses in Russia are now given the heartrending choice of either abandoning their faith or facing punishment for practicing it," said Rachel Denber, deputy Europe and Central Asia director at Human Rights Watch.
Russia's Justice Ministry said Jehovah's Witnesses "violate Russia's law on combating extremism" and their pamphlets incite hatred against other groups.