Spooneybarger was drafted by the Atlanta Braves in the 29th round of the 1998 Major League Baseball Draft and spent three seasons in the minors before making his major league debut with the Braves on September 5, 2001. Spooneybarger spent most of the 2002 season in the majors recording a 2.63 ERA in 51 games for the Braves. On November 18, 2002, Spooneybarger was traded to the Florida Marlins along with minor league pitcher Ryan Baker for Mike Hampton.
He started 2003 in the majors appearing in 33 games before going on the disabled list with elbow tendinitis. Before beginning a rehabilitation assignment, he was forced to have Tommy John surgery and miss the entire 2004 season. On July 20, 2005, while rehabilitating, he left the game in obvious pain and later learned he would have to undergo Tommy John surgery for a second time. The Marlins released him after the 2005 season and Spooneybarger would be out of professional baseball for the next two years.
Spooneybarger plays in a rock band called Mad Ink with former Marlins teammate A. J. Burnett. The group is so named because Burnett and Spooneybarger both sport many tattoos.