Yonhap news agency cited officials saying that soldiers fired about 20 rounds before the craft turned back.
Earlier, South Korea's president urged China to impose the strongest possible sanctions against North Korea, following its apparent nuclear test.
Pyongyang claims it has tested a hydrogen bomb.
That claim is doubted by experts, who say the blast, though probably nuclear, was not big enough to have been a thermonuclear explosion.
In a country as impoverished and isolated as North Korea, drone technology is the last thing one might expect from the military.
But on Wednesday South Korean troops spotted a surveillance drone flying near a front line observatory. The military in Seoul said the unmanned craft flew in from the north and crossed into the Demilitarised Zone. After soldiers fired warning shots, the craft turned back.
The military believes that the drone was launched by the North to identify South Korean troop positions that have been bolstered since North Korea's nuclear test a week ago.
Earlier in the day, propaganda leaflets carried by giant balloons from the North were also found near and in the South Korean capital Seoul. Some of the messages demanded that South Korean loudspeaker broadcasts across the border, stop. They were restarted in retaliation for the North's nuclear test last week.
In her annual press conference, President Park Geun-hye said the international community's response to North Korea "must differ from the past", without giving details.
She said new sanctions on Pyongyang must go further than before, with China's support crucial. She also warned of possible further action by North Korea, including "cyber terrorism".
China, North Korea's closest ally, has repeatedly condemned North Korea's nuclear tests but is often accused of doing little to try and stop them.
Ms Park stressed China's past statements but added: "I am certain that China is very well aware if such a strong will isn't followed by necessary steps, we will not be able to stop the North's fifth and sixth nuclear tests and we cannot guarantee true peace and stability on the Korean peninsula."
"I believe the Chinese government will not allow the situation on the Korean peninsula to deteriorate further."
Last week US Secretary of State John Kerry also urged China to take a tougher line, telling his Chinese counterpart the relationship with North Korea cannot be "business as usual".
President Park also spoke about the steps South Korea was taking with the US to "neutralise North Korea's provocative actions" including additional deployments of American military assets on the Korean peninsula.
Answering a question about whether Seoul would consider ending its involvement in the jointly-run Kaesong industrial zone, just north of the border, Ms Park said its future depended on Pyongyang's actions.
Seoul has already limited access to Kaesong from the South, to only those directly involved in its operations.
South Korean soldiers have fired warning shots at a suspected North Korean drone flown across the heavily fortified border.