Putin visited the Central Election Commission, handing over his passport and 300,000 signatures required by Russian legislation for those running as independent candidates.
The 65-year-old strongman, who will face only token opposition candidates, will extend his term until 2024, making him the longest-serving Russian leader since dictator Joseph Stalin.
A day earlier more than 600 celebrities, politicians and sports figures had gathered in Moscow to formally nominate Putin.
The Russian strongman skipped the ceremony, with the Kremlin citing his busy schedule.
Earlier this week electoral bosses barred top opposition leader Alexei Navalny from running against Putin, citing a controversial embezzlement conviction which he says is politically motivated.
"How do they look their children in the eyes?" Navalny asked on Facebook, referring to the outpouring of support for Putin, who was first elected president in 2000.
Putin instead met with children to open a Christmas tree on a square inside the Kremlin walls.
Candidates running against Putin include veteran ultra-conservative politician Vladimir Zhirinovsky, Communist Party candidate Pavel Grudinin and a former socialite turned liberal journalist Ksenia Sobchak.
Navalny, who is seen by many as the only Russian opposition leader who stands a chance of challenging Putin, has called for a boycott of the polls.
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