Lee led the South Korean men's national football team to a gold medal in the Incheon Asian Games in October last year. The country won its first gold in the Asian Games event in 28 years.
During a meeting of its technical committee earlier in the day, the Korea Football Association (KFA) named Shin Tae-yong, an assistant coach of the senior national team, to fill the post vacated by Lee.
The KFA said Lee was diagnosed with an acute form of leukemia.
South Korea's national football team won the bronze medal at the 2012 Summer Olympics in London.
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