The pair greeted each other warmly ahead of the talks, near the port city of Vladivostok in Russia’s far east.
The leaders reportedly discussed denuclearisation, with Mr Putin offering to support efforts to normalise North Korean-US relations.
Talks between those two powers stalled following a February summit between Mr Kim and US President Donald Trump.
Speaking after the meeting with Mr Putin, Mr Kim said the two leaders had a “very meaningful one-on-one exchange of opinions on issues of mutual interest and current issues”.
Mr Putin said the pair had discussed relations between the two Koreas, “and what we can do so that there are good prospects for an improvement in the situation”.
Speaking ahead of the meeting, Mr Kim said he hoped for “a very useful meeting in developing the relationship between the two countries, who have a long friendship and history, into a more stable and sound one”.
Mr Kim greeted Russian officials warmly when he arrived by train on Russky Island on Wednesday.
The North Korean leader was entertained by a brass band before he got inside a car flanked by bodyguards, who – in now familiar scenes – jogged alongside the vehicle as it departed.