The North's state-run Korean Central News Agency published a rare personal message from Kim, which said, "I congratulate you on your re-election as the President of the Russian Federation."
He went onto say, "Your re-election is a sign of great support and confidence that your people have in you."
Kim acknowledged the friendship and cooperation between Moscow and Pyongyang, expressing his hope to deepen and develop their ties.
"I wish you great achievements in your efforts to build up a stronger Russia," his message said.
Upon Putin's latest electoral victory, KCNA reported on the event, saying "Vladmir Putin has been selected again [as president] due to the overwhelming support of the majority."
Russia and North Korea's ties stretch before the 1950-53 Korean War, when the Soviet Union supported regime founder Kim Il Sung. Moscow then backed the regime with economic and military assistance throughout the Cold War.
The two states maintain their political and economic ties to this day, with Russian diplomats having opposed strong sanctions on North Korea, while supporting a peaceful resolution of the North's nuclear crisis.
On Tuesday, Russian media reported that Moscow "is ready for dialogue with all parties concerned" to normalize the situation on the Korean Peninsula, citing a high-ranking Russian foreign ministry official Andrei Kulik.
Kulik said Russia "hails the North Korean leadership's steps toward establishing inter-Korean dialogue and cooperation," including the North's participation in the Pyeongchang Winter Olympics and its reception of South Korean President Moon Jae-in's envoys earlier this month.
The envoys announced, after their meeting with Kim Jong Un, that the North Korean leader would hold talks with his South Korean and U.S. counterparts.
"Russia has always been speaking in favor of comprehensive settlement of the Korean Peninsula's problems, including the nuclear problem, by diplomatic means and with due account of legal interests of the sides," Kulik said, according to Russia's TASS news agency.