The meeting follows the official trip to the Winter Olympics in Pyeongchang by Kim Jong Un's sister, Kim Yo Jong.
The delegation, which is made up of 10 senior officials, had dinner with the North Korean leader in the latest step towards rapprochement on the divided peninsula.
It followed the trip to the Winter Olympics in Pyeongchang by Mr Kim's sister, Kim Yo Jong, which made her the first member of North Korea's ruling family to travel to the South since the end of the Korean War.
She met with South Korean President Moon Jae-in during a landmark event in which athletes from the two Koreas marched together and even competed in a joint women's hockey team.
Mr Moon was invited to the North by Ms Kim for a meeting with her brother and, while he has not yet accepted the offer, he sent the special envoy to Pyongyang on Monday in the hope of encouraging the rogue state to hold talks with Washington.
US Vice President Mike Pence was due to attend a historic meeting with North Korean officials at the Games on 10 February, but it was called off by Pyongyang after he condemned the regime's human rights abuses.
It was the latest clash in a war of words that has heightened fears over global security, with US President Donald Trump and Mr Kim having spent much of the last year trading threats of nuclear conflict.
South Korean national security adviser Chung Eui-yong, who is among those to have travelled as part of the special envoy, said Seoul was determined to help broker talks between the two countries.
"We plan to hold in-depth discussions for ways to continue not only inter-Korean talks but dialogue between North Korea and the international community, including the US," he said before the meeting.
"We will deliver President Moon's firm resolution to denuclearise the Korean peninsula and to create sincere and lasting peace."
Mr Chung is on the trip with the country's spy chief Suh Hoon and a number of other delegates, with none having travelled to the North since its former intelligence boss visited in December 2007.
They will fly to Washington on Wednesday to explain the outcome of the talks, knowing that the Trump administration has ruled out sitting down with Pyongyang so long as it harbours nuclear ambitions.