Maloney played college baseball at the University of Mississippi, and was drafted by the Philadelphia Phillies in the 3rd round (97th overall) of the 2005 Major League Baseball Draft. On July 30, 2007, he was traded to the Reds for Kyle Lohse.
Maloney made his Major League debut on June 6, 2009 against the Chicago Cubs. In that game, Maloney allowed six hits and two runs while striking out four in the Reds' 11th-inning 4-3 victory. He is the pitcher to give Johan Santana his first major league career homerun on July 6, 2010.