The first of the new generation submarines, which will be the country's main nuclear deterrent in coming years, entered into service in the Navy on Thursday.
The Borei-class missile cruiser raised the flag in a ceremony in the Arctic port of Severodvinsk.
"This event ... confirms the seriousness of our intentions to upgrade the Army and the Navy," President Vladimir Putin said.
Putin didn't attend the ceremony, however, and made his statement in a video linkup with Defense Minister Sergei Shoigu.
Putin spoke from a nearby naval base in Severomorsk, where he bestowed a medal on another warship.
The Yury Dolgoruky submarine is also the first to have the latest Bulava intercontinental missile onboard. The missile suffered multiple failures in tests that dragged on for years.
Sea trials began in June 2009, but the submarine experienced several technical defects that repeatedly delayed its commissioning, according to industry news portal Naval-technology.com.
Putin said another seven Borei-class submarines will join the Navy by 2020, Interfax reported. The Navy will also receive eight Yasen-class submarines by then, he said.
The Sevmash shipyard, based in Severodvinsk, will be the lead contractor for the warships, he said.
Shoigu said in an Interfax report that there would be seven Yasen-class submarines for the Navy — one less than Putin stated.
The Navy has already ordered three more Borei-class submarines: Alexander Nevsky, Vladimir Monomakh and Knyaz Vladimir.
Built at an estimated cost of 23 billion rubles ($750 million), the Yury Dolgoruky is 170 meters long and 13.5 meters wide, with a diving depth of 450 meters.
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