The visit of the archbishop to the Communist country takes place in an environment marked by tensions between both Asian nations.
The 70-year-old archbishop crossed the border Wednesday morning after receiving approval from Pyongyang and Seoul, a spokesperson of Seoul's ministry of unification told Efe.
According to the spokesperson, he came in order to meet with the South Korean Catholic workers in the Kaesong industrial area, the only valid joint project between two Koreas.
This is the first time that a cardinal of South Korea, where Catholicisim is the third most practised religion, has travelled to the neighbouring Communist country, which has no religion.
In addition to touring the industrial area, the cardinal is also scheduled to meet with the directors and officials of the South Korean factories in Kaesong before his return Wednesday evening, Yonhap news agency quoted a spokesperson of the Archdiocese of Seoul.
It is not known if archbishop Yeom, who also occupies the charge of apostolic of Pyongyang, will hold a mass in the industrial area.
The unusual visit of the South Korean cardinal to North Korea comes amidst tension between the two Koreas, whose relations have seriously deteriorated since March this year.
"We hope that the visit of the archbishop will be a positive step" at the moment to help improving the relations between North and South, the spokesperson of the unification ministry said.
The visit comes a few months ahead of Pope Francis's visit to South Korea Aug 14-18 to participate in the VI World Youth Day.
This will be the third time that a pope will travel to this Asian country and the first time in 25 years since Pope John Paul II visited in 1989.
South Korea has more than five million Cathloics (10.9 percent of the population), making it the third majority after Buddhists and Protestants in a country with 50 million inhabitants, half of whom are agnostics or atheists, according to the last official statistics of 2005.
Meanwhile, in North Korea the constitution guarantees the freedom of religion and there are some churches supervised by the state in Pyongyang. However, refugees who escape from this secretive country say that the regime strongly restrains any type of religious practice.