The agreement, which should see priests leading services in Pyongyang on major holy days from next year, followed a visit to the North Korean capital by South Korean bishops last week.
Pyongyang's state-run Korean Catholic Association (KCA) has no ties with the Vatican and is often referred to as the "Church of Silence" by Catholics in the South.
Although religious freedom is enshrined in the North's constitution, all religious activity is subject to extremely tight restrictions and completely banned outside of state-sanctioned institutions.
The South's Catholic Bishop's Conference of Korea (CBCK) said in a statement that priests from the Seoul archdiocese would visit the cathedral "on major Holy Days each year and hold a mass on a regular basis".
CBCK spokesman Lee Young-Sik told AFP the first visit was scheduled for Easter in March 2016.
"And then we will iron out details on how frequently they would visit and lead a mass there," Lee said.
In the early 20th century, Pyongyang was a regional missionary hub with scores of churches and a thriving Christian community that earned it the title of "Jerusalem of the East".
For North Korea's founder leader Kim Il-Sung, Christianity threatened his monopoly on ideology and had to be effectively eradicated, a goal he reportedly achieved with executions and labour camps.
The current regime allows Catholic organisations to run aid projects in North Korea, but direct relations with the Vatican are non-existent.
When Pope Francis visited South Korea last year, he held a special mass in Seoul dedicated to reunification of the two Koreas.
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