Finally, after years of diligence, Choi was appointed as Bucheon SK's head coach for the 2001 season.

However, though he had no problems with the team and was able to lead it fairly well, the Bucheon SK board decided to change their manager.

He continued his role as manager into the 2007 K-League season, before being replaced mid-season by Kim Ho.

On October 10, 2011, he signed a one-year contract to V-League's Hoàng Anh Gia Lai - one of the most popular football club of Vietnam.

In 2018, Choi left Gangwon to become the manager of K League 2 team Busan IPark, but resigned after only one season after failing to gain promotion.

Busan IPark finished third in the K League 2 but lost to FC Seoul in the promotion/relegation playoff final.