Harper, who is in Asia for a regional mini-tour that will include a nuclear summit in Seoul, also discussed the issue of illegal human smuggling with his Thai counterpart Yingluck Shinawatra.
Thailand was a staging point for migrant ships bringing Tamil asylum seekers to Canada in recent years.
But the main focus was on the economy as the two leaders announced they had agreed to launch "exploratory talks" on a free trade accord.
"This will be yet another part of Canada's ambitious trade agenda. As part of our economic action plan, we are positioning Canada for a stronger role in the world with trade patterns shifting," Harper said.
"Thailand has a rapidly industrialising economy with 65 million consumers. Canadian businesses are already flourishing here, particularly in IT, agriculture and clean technology, and Canada is rapidly becoming an investment destination of choice for Thai businesses."
Harper was accompanied by his foreign affairs and trade ministers, as well as a delegation of business executives, as he sought to boost cooperation with the trade-dependent Southeast Asian economy.
Yingluck said the two countries aimed to raise relations to a "higher level."
She added: "Thailand also looks forward to welcoming Canadian investors to our electronics, machinery, automobile and information technology industry as well as cooperation on alternative and clean energy, environmental protection and biotechnology."
On March 25-26, Harper will make his third visit to Japan, Canada's fifth largest trading partner. In South Korea on March 26-27, Harper will join leaders of 53 other nations for a nuclear security summit.