The North Korean drone was flying dozens of meters (yards) south of the border and turned back to the North after the South fired shots, South Korean defense and military officials said, requesting anonymity because of office rules. The shots did not hit the drone.
North Korean drone flights across the world's most heavily armed border are rare, but have happened before, AFP said.
North Korea has in recent years touted its drone program, a relatively new addition to its arsenal. In 2013, state media said North Korean leader Kim Jong Un had watched a drone attack drill on a simulated South Korean target.
In 2014, Seoul officials discovered what they called several North Korean drones that had flown across the border. Those drones were crude and decidedly low-tech, but were still considered a potential new security threat.
Animosity has been high since the North's claim on Jan. 6 that it had tested a hydrogen bomb. There is widespread skepticism over the H-bomb claim, but whatever the North detonated underground will likely push the country closer toward a fully functional nuclear arsenal, which it still is not thought to have. The North previously conducted atomic bomb tests in 2006, 2009 and 2013.
Seoul said Wednesday that North Korea had also flown balloons with thousands of leaflets across the border, some of them describing South Korean President Park Geun-hye and her government as "mad dogs."
Park on Wednesday urged North Korea's only major ally, China, to help punish Pyongyang for its nuclear test with what she called "the strongest" possible international sanctions that can force change in the North.