In July 2004, Choi was selected for the South Korea national junior team as a pitcher and participated in the 2004 World Junior Baseball Championship held in Taiwan. Choi started South Korea's first match in the preliminary round, and pitched 5 innings and gave up a run, leading his team to a 5-2 victory over Italy. South Korea eventually won the bronze medal at the competition.
In December 2004, he was named best high school batter of the year.
Signed by the SK Wyverns, Choi made his pro league debut in the 2005 season. He was successful as both a starting pitcher and a slugger in high school, but finally decided to be a full-time batter for his pro career.
As a third baseman, he had several mediocre seasons, but broke out in 2007 when he hit 109 hits, 16 home runs and batted .267.
In 2008, Choi helped his team to become 2-time Korean Series Champions, and he was finally named the series MVP.