Putin received the certificate and a taekwondo uniform at a ceremony in Seoul before wrapping up his visit to South Korea yesterday.
While the taekwondo grade is symbolic, Putin has earned a black belt in judo, another martial arts discipline.
The federation officials said they awarded Putin the 9th degree black belt title in recognition of his efforts to foster sports in Russia.
The same federation awarded UN Secretary General Ban Ki-moon a 10th degree black belt in taekwondo.
Russia has recently hosted a global martial arts competition in St Petersburg.