Alexander Sokolov worked at the RBK news agency when he was arrested in June 2015 on suspicion of participating in a banned extremist group.
The journalist denied any wrongdoing, saying his prosecution is due to an investigative report published two weeks earlier on government overspending on a project to build a new space port.
Sokolov's conviction today came as two other men also received jail sentences in the same case.
The court convicted Sokolov over his involvement in a group called "For a responsible government" which has campaigned for a referendum on a new law that would make officials accountable.
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But they said the group was cover for another organisation -- banned as extremist in 2010 -- which called for the violent overthrow of the government.
Sokolov denied any of his actions were criminal and said he would appeal the conviction.
"According to this decision, the idea itself of a referendum is seen as extremist," he said, Russian agencies reported.
Russia's media community and international media rights groups have spoken out in his defence.
Reporters Without Borders said the charges against him were "unsubstantiated" and denounced the "arbitrary" nature of the country's anti-extremism laws.
The journalist has worked for RBK since 2013. It is a respected publication known for numerous investigations of sensitive subjects, such as Russia's involvement in the conflicts in eastern Ukraine and Syria.
Sokolov also wrote an economics dissertation about the effectiveness of Russia's state companies, in which he pointed to systematic corruption and theft of budget funds.
Rights groups have long called for a reassessment of Russia's controversial anti-extremism laws, which they say allow courts to hand down lengthy jail sentences to people who simply shared information on the internet.
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