Kim left Pyongyang accompanied by top arms industry and military officials and the foreign minister.
The train pulled into Khasan station - the main rail gateway to Russia’s Far East from North Korea.
The Korean leader has made just seven trips away from his country in his 12 years in power. Four of those trips were to the North’s main political ally, China.
Kremlin spokesman Dmitry Peskov said: “It will be a full-fledged visit. There will be negotiations between two delegations, and after that, if necessary, the leaders will continue their communication in a one-on-one format.”
US officials said arms talks between Russia and North Korea were on the agenda with Kim and Putin likely to discuss providing Russia with weapons for the war in Ukraine.
Meanwhile, Putin has arrived in Vladivostok for the plenary session of the Eastern Economic Forum.
Mr Peskov said that his meeting with Kim would come after the forum and that no news conference by the leaders is planned, according to Russia news agencies.
Mr Peskov said Russia’s national interests would dictate its policies.
He added: “As you know, while implementing our relations with our neighbours, including North Korea, the interests of our two countries are important to us, and not warnings from Washington.”
Washington renewed its warnings to Pyongyang not to sell arms to Russia that could be used in the Ukraine war, urging the North to abide by its promise not to provide or sell weapons to Russia.
The US State Department said any transfer of arms from North Korea to Russia would violate UN Security Council resolutions, which ban any arms transactions with North Korea.
State Department spokesperson Matthew Miller said: “We, of course, have aggressively enforced our sanctions against entities that fund Russia’s war effort ... and will not hesitate to impose new sanctions appropriately.”