A senior Agriculture Ministry official confirmed the second case in a pig farm in the southeast province of North Gyeongsang, but played down the threat.
"We believe the possibility of the disease growing into a nationwide outbreak is slim," the head of the ministry's livestock policy bureau, Kwon Jae-Han, told reporters.
He stressed that both cases involved the type "O" strain of the disease which South Korea vaccinates widely against.
"Still, it is too early to completely let our guard down as outbreaks of the disease have also been reported in China and North Korea and some animals here may not have been vaccinated," Kwon said.
Out of 2,000 pigs, eight had shown symptoms. He said, adding that the farm had been effectively quarantined.
The first case had been reported on July 24 at another pig farm, 70 kilometres (40 miles) away in the same province.
Only two months ago, South Korea was declared free of the disease at a meeting of the World Organisation for Animal Health in Paris.
The 2011 outbreak hit the entire Korean peninsula and resulted in the culling of nearly 3.5 million cattle, pigs and other animals in South Korea alone.
The Seoul government estimated the cost of that outbreak at $2.6 billion.
Foot-and-mouth disease affects cloven-hoofed animals such as cattle, pigs, deer, goats and sheep.
North Korea suffered an outbreak in February this year, triggering a rare offer of vaccine and medical equipment from the South.