Witnesses said other protestors and emergency responders moved quickly to douse the flames and the man was taken from the scene by stretcher.
His precise condition was not known.
The Yonhap news agency identified him as an 81-year-old South Korean man.
Close to 1,000 protestors had gathered outside the embassy ahead of this Saturday’s 70th anniversary of the end of Japan’s 1910-45 colonial rule over the Korean peninsula.
South Korea says Japan has still not done enough to atone for the forced recruitment of South Korean women to work in Japanese military brothels as so-called “comfort women.”
Japan insists the issue was settled in the 1965 bilateral agreement that restored diplomatic ties between the two nations, which saw Tokyo make a total payment of $800 million in grants or loans to its former colony.
The issue has strained relations between Seoul and Tokyo for years with South Korean President Park Geun-Hye saying there can be no meeting with Japanese Prime Minister Shinzo Abe until Japan makes full amends.