The local currency was traded at an average of 1,030.57 won per 100 yen in January, down 31 won from the previous month, according to the Bank of Korea.
The January reading marked the lowest level since November 2016, when the won hit 1,076.82 against 100 yen.
The US dollar serves as the benchmark for the won-yen cross rate.
The yen's strength came amid concerns about the global economic downturn as economic uncertainty heightened due mainly to a trade spat between the United States and China and a recent US government partial shutdown.
A stronger yen puts Korean exports at an advantage in price competitiveness in global markets.
South Korea's exports fell 5.8 percent on-year to $46.4 billion last month, data by the trade ministry showed.
But exports of autos and steel, which compete against Japanese rivals in global markets, rose 13.4 percent and 3.3 percent, respectively, it said.