After ending his player career, Kim became a manager. He managed April 25 Sports Team until 2007, when he became the manager of North Korea national team. In 2009 he led the team as it qualified for the 2010 World Cup, their first since 1966.
After a disappointing showing at the World Cup, Kim faced harsh criticism upon his return to North Korea. Radio Free Asia reported that he was publicly shamed and condemned for hours in front of 400 people, including the North Korean sports minister.
At the same event, the team members were commanded to individually criticize their coach, who was accused of betraying General Kim Jong-un, the country's heir apparent. The report also mentioned that he had been stripped of his membership in the Workers' Party of Korea and forced to work hard labor on a construction site as punishment. This rumor later turned out to be false after an investigation by FIFA into the matter.