Clinton, who is on a visit to the South Korean port city of Busan to attend a global forum on aid effectiveness, made the remarks when she held talks with South Korean Foreign Minister Kim Sung-hwan.
Ratification of the trade pact in both nations was "hard work," Clinton told Kim. "I remember one of those sayings that anything worth doing is hard to do."
South Korea and the U.S. are working to get the deal, which will eliminate 95 percent of tariffs between the two nations, to take effect on Jan. 1.
The two economies reached the deal in 2007, but ratified it about four years later amid protests from farmers and civic groups, which argue that the deal will only favor big businesses.
Clinton arrived in Busan on Tuesday night to take part in the Fourth High Level Forum on Aid Effectiveness, which also includes U.N. Secretary-General Ban Ki-moon and OECD Secretary-General Angel Gurria.
In a statement, the U.S. state department said, "Clinton's participation reflects the United States' strong political commitment to development as a key pillar of global security, prosperity and democratic progress."
More than 3,000 government delegates and leaders of international organizations are in attendance at the three-day conference that started Tuesday.
The conference aims to assess progress in improving the handling of global aid funds, following previous meetings in Paris, Rome and Accra, Ghana and set forth a new paradigm for global development aid, Seoul officials said.
After a brief stay in Busan, Clinton will head to Myanmar, marking the first visit by a U.S. secretary of state there in over half a century, the statement said.