Kim's armored train departed the Far Eastern port city of Vladivostok a day after talks that saw Putin back the North's need for "security guarantees" in its standoff with the United States, AFP wrote.
The official Korean Central News Agency reported that Kim told Putin the US had adopted a "unilateral attitude in bad faith" at a summit with US President Donald Trump two months ago in Hanoi.
"Peace and security on the Korean peninsula will entirely depend on the US future attitude, and the DPRK will gird itself for every possible situation," Kim was quoted as saying.
The Kim-Trump summit broke down in late February without a deal, after cash-strapped Pyongyang demanded immediate relief from sanctions but the two sides disagreed over what the North was prepared to give up in return.
Russia has called for the sanctions to be eased, while the US has accused it of trying to help Pyongyang evade some of the measures – accusations Moscow denies.
Just a week ago, Pyongyang demanded the removal of US Secretary of State Mike Pompeo from the stalled nuclear talks, accusing him of derailing the process.
On Thursday, Putin emerged from the meeting saying that like Washington, Moscow supported efforts to reduce tensions and prevent nuclear conflicts.
But he also insisted that the North needed "guarantees of its security, the preservation of its sovereignty".
It was "what the North has been saying all along" said Kim Keun-sik, professor of North Korean Studies at Kyungnam University, adding that Putin's support for Pyongyang's stance was the "biggest prize" Kim won in Vladivostok.
Putin flew on to another summit in Beijing the same day, while Kim stayed in Vladivostok and had been due to take part in a series of cultural events.
The summit saw both leaders saying they were looking to strengthen ties that date back to the Soviet Union's support for the founder of North Korea, Kim's grandfather Kim Il Sung.
Kim said he hoped to usher in a "new heyday" in ties between Pyongyang and Moscow.
The North Korean leader invited Putin to visit "at a convenient time" and the invitation was "readily accepted", KCNA said.
The meeting was Kim’s first with another head of state since returning from the summit with Trump.
It followed repeated invitations from Putin after Kim embarked on a series of diplomatic overtures last year.
Since March 2018, the North Korean leader has held four meetings with Chinese President Xi Jinping, three with South Korea's Moon Jae-in, two with Trump and one with Vietnam's president.
Soon after his first election as Russian president, Putin sought to normalize relations with Pyongyang and met Kim Jong Il – the current leader's father and predecessor – three times, including a 2002 meeting also held in Vladivostok.
China has since cemented its role as the isolated North's most important ally, its largest trading partner and crucial fuel supplier, and analysts say Kim could be looking to balance Beijing's influence.