Jones attended North Carolina State University, where he studied English and swam for the NC State Wolfpack swimming and diving team in the National Collegiate Athletic Association (NCAA) competition from 2003 to 2006. He turned professional in the summer of 2006, after signing with Nike and burst onto the scene shortly after at the 2006 Pan Pacific Swimming Championships where he set a meet record in the 50-meter freestyle with a time of 21.84 seconds. He also swam a leg (split of 47.96) in the world record breaking 4×100-meter freestyle relay along with Michael Phelps, Neil Walker and Jason Lezak. In 2007, he also won a gold medal in 4×100-meter freestyle relay with the same teammates in the 2007 World Aquatics Championships.