Kim was greeted by senior officials and an honor guard at a train station, according to the report which described his trip as a significant step in strengthening North Korea-Russia relations.
His trip and the summit with Russian President Vladimir Putin received global attention since the leader seldom leaves his country and drew concerns over possible arms trade and technology transfer with Russia.
Against that backdrop, South Korea on Tuesday summoned Russia's ambassador to warn Moscow against any military cooperation with North Korea.
Seoul and Washington have said military cooperation between North Korea and Russia would violate UN Security Council resolutions and urged against it.
Last week, the head of the reclusive state during his lengthy trip visited a Russian fighter jet factory under Western sanctions and praised the country's aviation technology.
He also met Defence Minister Sergei Shoigu, who showed the North Korean leader Russian nuclear-capable strategic bombers, hypersonic missiles and warships.