The famously reclusive Kim rarely meets officials from other countries. The man he will meet, Unification Minister Chung Dong-young, received the invitation while he was out on a morning jog during a visit to Pyongyang, North Korea's capital.
The expected talks - announced by a ministry spokesman in Seoul - come as delegates from South Korea are in Pyongyang to mark the fifth anniversary of a landmark summit between Kim and then South Korean president Kim Dae-jung.
"The minister plans to meet Chairman Kim Jong-il today. But we can't give you details about the place or time," the spokesman said by telephone in Seoul.
Kim's main official title among the many he holds is chairman of the National Defence Commission.
The timing of the meeting is significant, although it was too early to say whether Kim would use the encounter to make a breakthrough announcement or pass a message.
There is growing concern over whether North Korea will return to stalled six-party talks on ending its nuclear weapons programme. The last round of talks was in June last year.
Washington has said the North has told US officials Pyongyang will return, but the communist state did not set a date. The talks bring together the two Koreas, China, Japan, Russia and the US.
South Korea is keen to see the
North return to nuclear talks
One analyst said Kim may use the meeting to deliver a message to South Korean President Roh Moo-hyun.
"The North may say that they appreciate Roh's efforts for the six-party talks. And there is a possibility that Kim will say he is considering a summit meeting with Roh," Paik Hak-soon of South Korea's Sejong Institute said.
The North's leader promised at a summit in 15 June 2000 to visit the South but has yet to do so.
Chung would be only the second South Korean senior official to meet Kim since the 2000 summit of the leaders of the North and South, the ministry said. In April 2002, Kim met a South Korean special envoy.