In the middle of the season, he changed his free skating from "The Planets" to "The Phantom of the Opera", which was shown at the Korean Nationals. At the nationals, with total score of 206.88, Lee became the first Korean male skater who scored over 200 points in domestic competitions. In February, he placed 14th at the 2013 Four Continents Figure Skating Championships in Taipei. In March, he placed 16th at the World Junior Championships in Sofia, Bulgaria.