On January 23, 2006 the Chicago Cubs signed Miller to a one-year, one million dollar contract, with $1 million more in incentives. Miller made his first start of the 2006 season on September 9. Overall, Miller made five starts in 2006, finishing with a record of 0-2 with a 4.57 ERA. He filed for free agency after the season.
On November 9, 2006 Miller signed an incentive-laden, 1.5 million dollar one-year extension to stay with the Chicago Cubs under new manager Lou Piniella. However, after three unsuccessful starts where he compiled a 10+ earned run average, Miller was once again placed on the DL in July of 2007. He was given his unconditional release from the team one month later.
In an eight-year career (through the end of the 2006 season), Miller has compiled a 62-45 record with 743 strikeouts and a 4.00 ERA in 880.2 innings.