The debate comes as the president, Roh Moo-hyun, passes the three-year mark of a single five-year term, and he said he would focus the remainder of his time in office on reducing social disparity and on reaching a free trade agreement with the US.
"Those will be the biggest issues of the remaining term, and both will probably be very tough," he told reporters.
Free trade talks between the $72.5bn trade partners are to start in May.
South Korea is the world's most wired country, and most homes are connected by broadband. Roh, a self-educated former lawyer, is himself a proficient internet user.
He will field questions from the public posted on five major internet portals that will carry the debate with a pre-selected panel, his office said in a statement on Sunday.
Roh has made it a major policy objective to push for balanced
development in South Korea, where income and industrial disparities remain a main source of political and social conflict.
He has said globalisation and free trade can be an argument for, not against, reducing disparities and poverty.
Roh expressed regret at attempting some of the controversial political moves in the past three years, including an unsuccessful proposal to form a coalition government with the opposition last year.
"I suffered great (political) damage because of that, and the president's credibility with the public also suffered greatly," he said in a letter to the public, released on Sunday.
He also criticised the framework of the single-five year term, saying its timing did not match other key elections and made the job of running the country difficult.
"The president's term of five years is a bit too long," he said. "It would be better not to have elections in the middle of a term."
Roh: The president's five-year
term is too long
South Korean parliament sits for four-year terms, while local elections held separately pick heads of provinces, counties, cities and their assemblies every four years.
South Koreans go to the polls on 31 May to pick local representatives. National parliament was elected in 2004.
Roh denied he was proposing a constitutional amendment to allow presidents successive four-year terms to overlap with the terms of members of parliament and local government heads.
"The game of elections is a fight for votes and beyond substance," he said. "Elections can be about getting judged on policy, but they are also at least partly a game of fooling the voters."