He replaces Hwangbo Kwan, who, along with head coach Hong Myung-bo, stepped down after the Koreans managed only one point in a group stage exit at the recently concluded World Cup in Brazil.
"I decided someone had to do it, and so I am back after some 10 years," Lee, 54, was quoted as saying by the Yonhap News Agency.
"The most pressing matter now is obviously to name the new national team head coach.
"I am not yet at a point where I can say whether we will bring in a South Korean coach or a foreign coach."
Twice winners South Korea have been drawn in Group A of the 2015 Asian Cup in January alongside hosts Australia, Oman and Kuwait.
(Reporting by Patrick Johnston; editing by Amlan Chakraborty)