The Moscow city court accepted the arguments of Russia's justice ministry that as the term "Scientology" is a registered US trademark, the Church cannot be considered a religious organisation.
The organisation plans to appeal, reports said.
The court set a six-month timescale for the Church to close, the ministry said.
Created by science fiction writer L Ron Hubbard in 1954 and based in Los Angeles, California, the Church of Scientology has generated controversy around the world.
Critics say that it is a cult and that it scams its members, while supporters maintain that it provides spiritual support to its followers.
A Russian court has ruled that the Moscow branch of the Church of Scientology should be dissolved.