Jones moved to Rutherford, New Jersey, in 1981 and played in Rutherford Little League from 1982 to 1984. In 1991, he was drafted by the Milwaukee Brewers in the 44th round as a draft-and-follow. He signed prior to the 1992 draft and was assigned to Helena in the Pioneer League (rookie), where he went 5–4.
Jones operated his own baseball academy named Bobby Jones Sports in Montville, New Jersey, until it was closed down. Jones also spent time as the pitching coach for both the Don Bosco Prep and Montclair Mounties varsity baseball teams. He also worked with the Academy of Pro Players located in Hawthorne, New Jersey, as a pitching instructor.
Jones made his major league debut at Shea Stadium against his boyhood team, the New York Mets. He got a no-decision in that game, won by the Mets, but earned the victory in his next start, against the Houston Astros.
Jones spent all of 1998 and most of 1999 with the Colorado club, splitting his time between the starting rotation and the bullpen. In early 2000, the Rockies traded Jones to the Mets, meaning he and Bobby J. Jones were now on the same roster. The two had faced each other in a 1999 game, with the Rockies' pitcher earning the victory.
