Kim and Guterres attended a dinner ahead of the opening of the Winter Olympics in Pyeongchang.
"He did have a brief exchange with president Kim," said UN spokesman Farhan Haq.
Guterres reiterated "his expectation and hope that all parties will use dialogue to achieve the peaceful denuclearization of the Korean peninsula," he added.
Kim is leading the North Korean delegation to the Olympics that also includes Kim Yo Jong, the younger powerful sister of North Korean leader Kim Jong Un.
The exchange with Kim however was the highest-level meeting between the UN chief and North Korea.
Guterres has met with the foreign minister and Pyongyang's ambassador to the United Nations. Kim holds the title of president of the presidium of the Supreme People's Assembly, making him technically the head of state.
The UN chief has been a strong supporter of the thaw in relations between Pyongyang and Seoul during the Olympics, which he maintains could provide the basis for a broader dialogue.
At an official lunch hosted by South Korean President Moon Jae-in, Guterres expressed his "total support" to Moon for establishing "a very important positive development in inter-Korean relations.
US Ambassador Nikki Haley has dismissed North Korea's decision to attend the Olympics as a "distraction," and Vice President Mike Pence skipped the dinner on Friday.
In December, Guterres dispatched UN political chief Jeffrey Feltman to Pyongyang for talks, but the envoy came back with no commitment from North Korea to hold negotiations on the nuclear standoff.
North Korea's race to build an intercontinental ballistic missile that could hit the United States with a nuclear warhead has raised fears of a devastating conflict.
Trump's administration has been adamant that North Korea must first freeze its military programs before talks can take place.
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