Mooney first played in the 2006 season and saw action in nine games, including a role on special teams. In 2007, Mooney played as a back-up in all 12 games.

In 2008, Mooney ran for a school record 1,339 yards in 12 games. In an overtime loss against Buffalo, Mooney rushed for 172 yards and two touchdowns including an 81-yard touchdown run. For his performance against the Bulls, who went on to beat undefeated Ball State for the MAC championship, Mooney was honored with a “helmet sticker” by ESPN. In a loss at Rice, Mooney picked up 61 yards in a touchdown run. Mooney scored four touchdowns in the 44–13 victory over Tulane. For this, he was bestowed West Point’s Black Death Award for “near perfect play”, named the Army Athletic Association Athlete of the Week, and nominated for the AT&T All-America Player of the Week honors.

Mooney played for the East squad in the 2009 East-West Shrine Game. He served three years as an Army officer before being granted a release to play professional football.

Mooney was signed by the Tennessee Titans on May 1, 2012 after going undrafted in the 2012 NFL Draft. After seeing modest playing time in the 2012 and 2013 seasons for the team, Mooney was waived by the Tennessee Titans on August 29, 2014.