[2] In 2009, Rooney replaced longtime UCF Knights head coach, Jay Bergman.
On June 21, 2010, Rooney signed a four-year contract extension with the university, making him the Knights head baseball coach through 2014.
From 1997–2003, Rooney was an assistant coach at George Washington, James Madison, Old Dominion and Stetson.
In 1997, he was pitching coach of the Cotuit Kettleers, a collegiate summer baseball team in the Cape Cod League.
[5][6] In 2004, Rooney joined the staff at Notre Dame under head coach Paul Mainieri.