The incident comes amid rising trade and political disputes between Seoul and Tokyo.
Police say the man, surnamed Kim, died while being treated in a Seoul hospital on Friday.
According to police, he ignited a fire inside his car parked in front of the building where the Japanese Embassy is located.
Police say Kim had told an acquaintance before the incident that he was trying to set himself ablaze because of his antipathy toward Japan.
South Korean police say a man has set himself on fire in front of the Japanese Embassy in Seoul amid rising trade disputes between Seoul and Tokyo.
Police say the man in his 70s ignited a fire inside his car parked in front of a building where the Japanese Embassy is housed on Friday.
Police say the man was taken to a hospital but didn't provide the status of his condition.
Media reports say he is unconscious.
The motive for his action wasn't immediately known. But it comes as ties between Seoul and Tokyo have plunged to their lowest point since Japan recently tightened export controls of some high-tech materials.
Police say suspected flammable materials were found in the man's car.