He played in Major League Baseball (MLB) for the Cincinnati Reds and Minnesota Twins.

Maloney started his career in 2005 with the short-season class-A Batavia Muckdogs, where he pitched eight games and went 2–1 with a 3.89 ERA.

He spent all of 2006 with the Lakewood BlueClaws, and was the South Atlantic League's Most Outstanding Pitcher for the season.

He started 21 games for the double-A Phillies and was named a mid- and post-season All-Star for the Eastern League after posting a 9–7 record with a 3.94 ERA.

He spent nearly a month on the DL with a strained right oblique muscle (7/18 to 8/7), and made one rehab start for the Gulf Coast League Reds.

He was in line for the win but the bullpen blew the one-run lead and the Reds eventually won 4–3 in 11 innings.

Although bothered by a blister on the middle finger of his throwing hand, he pitched much better in his third stint, going 2–1 with a 2.65 ERA.

He also became the first Reds pitcher to get a hit in his first Major League plate appearance since Scott Randal in 2003.

On February 15, 2013, Maloney signed a minor league deal with the Boston Red Sox.

Maloney signed with the Sugar Land Skeeters of the Atlantic League of Professional Baseball for the 2015 season.