Choi was appointed as assistant coach of FC Seoul in August 2006. In April 2011, he was promoted as the caretaker coach. After leading club to a fifth place, he was named as club's permanent coach in December 2012 and won 2012 K League. In 2013, Choi led the club to the final of the 2013 AFC Champions League. They drew all two matches of the final against the chinese club Guangzhou Evergrande but didn't get the title due to the away goals rule. Choi was named the AFC Coach of the Year.