Upon graduation from Seongnam High School, Ko was drafted by the Doosan Bears in the second round (17th overall) of the 2002 KBO Draft. He had several mediocre season, spending most of his time in the reserve team of the Bears.
In 2007, Ko batted .268, compiling a career-high 12 home runs, 119 hits and 66 RBIs while appearing all 126 regular-season games. He led the KBO league in runs (89), and 3rd in stolen bases (36). After the season, he won his first Golden Glove Award at second base.
In 2008, Ko batted .267 with a career-high 70 RBIs, 114 hits, 84 runs, 39 stolen bases and 9 home runs. He led the KBO league in walks (74), and ranked 3rd in runs, 4th in stolen bases and 13th in RBI.
Prior to the 2009 KBO season, Ko participated in the 2009 World Baseball Classic in March 2009. In the WBC, he batted .308 with 4 hit in 13 at-bats, sharing the starting second base position with Jeong Keun-woo. In Round 2, Ko smacked a solo home run off New York Mets starter Óliver Pérez in the bottom of the 5th inning to lead his team to an 8–2 victory over Mexico.