Humber made the Twins' Opening Day roster in 2009 as a long reliever. Humber struggled at the start of the 2009 season, pitching to a 12.46 ERA over innings, while giving up 11 hits and walking four batters. The Twins designated Humber for assignment on April 17, 2009 to make room on their roster for Juan Morillo, whom the Twins had claimed off waivers from the Colorado Rockies. Humber cleared waivers and the Twins assigned him to Rochester. The Twins recalled Humber in August 2009 due to an injury to Francisco Liriano, but outrighted him to the minor leagues ten days later. Humber was granted free agency after the 2009 season.