Earlier in June, a law was passed banning leading figures in extremist organizations from running in elections for five years.
Members at a lower level, as well as financiers, must also be able to be disqualified for three years.
Critics fear that the law thus also risks affecting the tens of thousands of people who have supported Navalny's network of donations.
At the end of April, Navalny's regional campaign network received a similar stamp.
On Wednesday, a court in Moscow decided to classify the organization as extremist, reports Reuters and AFP.
This means that the organization's work and those who work for them can be the subject of legal proceedings.
Activist, lawyer and blogger Navalny has made himself known for his sharp criticism of President Vladimir Putin and for his work against corruption.
Earlier this year, he was sentenced to three and a half years in prison for violating the rules of a previous conditional sentence of embezzlement.
The regime critic had refrained from reporting to his supervisor when he was in a coma in Germany after being poisoned with the Soviet-developed neurotoxin novitjok.
He has also been charged with other crimes, accusations that his supporters and many outside judges consider to be politically motivated.
Who is Alexei Navalny?