The Seoul-based International Vaccine Institute (IVI) said in a press statement that 3,000 children would be treated under a pilot project to be launched in early 2008.
The agency will soon finalise project details and also help the North improve its diagnosis capabilities, with IVI director general John Clemens to meet with North Korean officials in Beijing before month's end, it said.
The impoverished North has yet to introduce vaccines against the two diseases, which still pose a major threat to children in developing countries, the IVI added.
"These are devastating infections, with high mortality rates and high rates of permanent neurological disability among children who survive," Clemens said.
"We hope this is the beginning of our expanding partnership with DPRK (North Korea) authorities in the coming years."
IVI said it had organised a tour for North Korean vaccine experts in China and Vietnam in May to help them understand the agency's pilot project for the communist state.
Established as an initiative of the United Nations Development Programme in 1997, IVI is the world's only international organisation devoted solely to providing new vaccines for developing countries