After the 2002 season, Milwaukee traded Bako to the Chicago Cubs, where he spent two complete seasons; 2003 and 2004 were the only consecutive seasons that Bako spent with the same organization. Over his two years, he backed up Damian Miller and Michael Barrett, and was reunited with former Braves teammate Greg Maddux in 2004. In his first Chicago season, Bako batted .229 with 22 walks and 13 doubles; a 4-for-5 performance in his second game of the year was his best of the season. In that game, he batted three times against the Reds with the bases loaded, notching a triple, two singles and six RBIs. Bako batted only .203 for the Cubs in 2004. He hit one home run and eight doubles, displaying his defense with a .989 fielding percentage. His top performance that year was in the second game of a doubleheader against Florida, when he went 3-for-3 and batted in two runs.