Rooney was born September 13, 1975 in Baxter Springs, Kansas and was raised in Picher, Oklahoma. He went to Picher-Cardin High School. His first known band, Uncle Thumbtack, was formed in Miami, Oklahoma with Erin and Greg Fitzgibbon in 1992–1997. Rooney is currently the lead guitarist and a harmony singer in the American country pop trio Rascal Flatts. In addition to electric guitar, he plays the acoustic and bass guitars, as well as mandolin. Rooney was influenced by many guitarists including Chet Atkins, Eric Clapton and Jeff Beck.
Rooney's first band was Called Lost Cause which later became known as Uncle Thumbtack with Gregory Fitzgibbon (singer–songwriter and bass guitarist), Erin Fitzgibbon (singer–songwriter and acoustic guitarist), Colin Frayser (drums) and Jason Winnie (Rhythm Guitar) Joe Don (Lead Guitarist and back up Harmony). Joe Don frequently jammed with family member musicians Justin Speer, Tracy Conder, and Jeramy Essary (whom he later dedicated "I'm Moving On").
Rooney was involved in a two-year romance with Lyric Street labelmate Kassidy Osborn of SHeDAISY. The couple parted ways in 2003.
Rooney married former beauty queen—Miss Georgia USA 2001 and Miss USA 2001 2nd Runner-Up and 2005 Playmate of the Year—Tiffany Fallon on April 23, 2006. The couple was featured in the Playboy Cyber Club's celebrity photographer section, with the nude pictorial of Tiffany being shot by Joe Don himself. The couple had a son named Jagger Donovan Rooney on May 31, 2008.