The denomination says it has 175,000 members in Russian Federation - a country where it was persecuted during the Stalin era. "But they are seen as a good target".
The ban on the Jehovah's Witnesses in Russian Federation is significant partly because it is the first time that Russian Federation has banned an organized religious group, according to the United States Commission on International Religious Freedom (USCIRF). The Islamic State and Al Qaida are also banned in Russian Federation.
In February, investigators inspected the headquarters of the Jehovah's Witnesses in St. Petersburg, the independent Russian newspaper Novaya Gazeta reported.
The Jehovah's Witness denomination was organized in the 1880s by Charles Taze Russell in the United States.
In a Thursday ruling, the court upheld a government request to ban the group from operating on Russian territory.
"They pose a threat to the rights of the citizens, public order and public security", she told the court. Still, said Robert Warren, none of the evidence presented offered a justification for the ban.
Jehovah's Witnesses has said it would appeal the decision.
"The main problem that we face now is misuse of the anti-extremism law. I think it's really an embarrassment to Russia and it really sends a very negative message about the Russian authorities to the worldwide community". If the organization appeals it, the ruling will come into force as of the moment the appellate court pronounces its opinion or in 30 days' time.
Russia's Justice Ministry said Jehovah's Witnesses "violate Russia's law on combating extremism" and their pamphlets incite hatred against other groups.
Reese, though, conceded he had little hope of either avenue being successful.
The religious group's press service said its religious programs do not include banned materials and that officials have notified authorities whenever anyone brings such literature into their building.
But he admitted that he was unsure how those recommendations would be taken on board by President Donald Trump, whose administration's position on Russian Federation he described as being "in flux".
Jehovah's Witnesses believe in a distinct version of Christianity with its own interpretation of the Bible. The attorneys of the group in Russian Federation have confirmed that they will appeal the court's decision. "Put them in jail?"
Jehovah's Witnesses say the accusations are completely untrue.
"We will do everything possible", Mr. Cherepanov said.