The incident came as South Korean activists launched balloons containing leaflets condemning North Korean leader Kim Jong-un.
Pyongyang had warned of "catastrophic" consequences if Seoul allowed the activists to go ahead.
The two sides exchange periodic fire across their disputed maritime border but incidents on land are rare.
Yonhap, citing military officials, said the North fired towards the balloons and South Korea responded after some shots landed south of the border.
There was no immediate information on whether there were any casualties.
The clash came as North Korea marked the 69th anniversary of its ruling party.
Mr Kim, who has not been seen in public for more than a month, did not attend, according to a list provided by state media.
10 October 2014
South Korea started by launching balloons, the Norks retaliated with artillery, so the Southies did, too.
Posted by Brant at 11:30