The ruling could further heighten tensions between the NATO member and Moscow after relations hit their lowest level in recent years over Russian intervention in Ukraine.
Judge Regina Pociene said the handcuffed Nikolai Filipchenko "worked for the Russian federal security service (FSB) whose activities include intelligence outside of the Russian Federation."
She added that the 40-year-old used forged documents to conceal his real identity and had repeatedly crossed the border illegally.
Last year, prosecutors said he attempted to recruit security officials "in an attempt to install special listening devices" to bug President Dalia Grybauskaite at her home and office.
Filipchenko's lawyer Galina Kardanovskaja told reporters he "disagrees with the charges" but it was "too early to say" if he would appeal the verdict.
She added that Russian diplomats were providing her client with some money and literature.
Lithuanian authorities arrested Filipchenko in April 2015 on his way to Belarus on a train from the Kaliningrad region, Russia's westernmost outpost bordering Lithuania and Poland.
The verdict came a day after US President Donald Trump accused Russia of "destabilising" action in Ukraine and endorsed NATO's mutual defence pact during a keynote speech in neighbouring Poland.
NATO is deploying about 1,000 soldiers in each of the Baltic states and Poland in response to growing nervousness over Russian intentions.
The Kremlin has denied any territorial ambitions and claims that NATO is trying to encircle Russia.
Filipchenko is the second Russian citizen sentenced this year in Lithuania for espionage. In 2015, Russian courts sentenced two Lithuanian nationals for spying on Moscow.
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