Harper welcomed Kim Hwang-sik to Ottawa on Tuesday as the two countries marked half a century of bilateral relations.
The men met in Harper's Parliament Hill office prior to a ceremony to mark the start of the "year of Korea" in Canada next year.
Harper underlined the importance of the Canada's relations with South Korea, including 50 years of bilateral relations and the upcoming 60th anniversary of the end of the Korean War, which claimed the lives of 516 Canadians.
Harper lauded South Korea's massive economic growth in trade with Canada over the past half century.
"And yet, there remains between us massive and yet untapped economic potential and so it will take concerted efforts by both our countries to reap all of the benefits that this relationship can yield," he said at a gala in Ottawa to welcome Kim and mark the milestones in their bilateral relationship.
Earlier, the two leaders also discussed investment and energy issues.
Prior to Kim's arrival in Ottawa, Foreign Affairs Minister John Baird denounced North Korea for its plan to test a long-range ballistic missile in the coming weeks.
Baird said Canada considers the North Korean move provocative and a violation of several UN Security Council resolutions.
Harper said he hoped the two Koreas would one day be unified.
"I know all of us look forward to the day, it may seem far off, but it will come, when the lights of freedom turn on in North Korea, and the two Koreas can live as one, and in peace," he said.
The most recent of Harper's three visits to South Korea came in March to attend an international summit on nuclear security.
South Korea is one of several countries with which Canada is trying to negotiate a free trade deal.
The Harper government is in negotiations or in the exploratory stage of talks with most of the big economies in the world, including Europe, Japan, India, China and several Asian countries covered under the Trans-Pacific Partnership.
A major irritant with South Korea was removed in June when Canada dropped its challenge to the country's ban on Canadian beef imports.
Canada formally dropped its challenge to the World Trade Organization because South Korea restored access in January. South Korea originally banned imports of Canadian beef after the 2003 outbreak of bovine spongiform encephalopathy, commonly called mad cow disease.
The breakthrough that ended the ban came after Harper's bilateral meeting with South Korean President Lee Myung-bak at the G20 summit in Mexico this past summer.