In 1998-99 Cheltenham secured the Conference championship - their passport to the football league.

After two mid-table finishes in Division Three, Cheltenham finally won promotion to Division Two through the playoffs at the end of the 2001-02 campaign. Shortly after gaining promotion, Steve Cotterill departed Cheltenham to progress his career by joining Stoke City as manager. He stayed there for just 4 months prior leaving to become Sunderland's assistant manager, a job which he held for just five months. Cotterill returned to football management in June 2004 with Burnley. He is still currently manager there.

Meanwhile, Cheltenham replaced Cotterill with first-team coach Graham Allner who had won the Conference championship with Kidderminster Harriers in 1994. However he was dismissed in January 2003, after just six months in the job, with Cheltenham moving around near the foot of Division Two. Cheltenham turned to Bobby Gould, one of the most experienced managers in English football whose exploits include an FA Cup win with Wimbledon in 1988. Cheltenham continued to struggle and defeat in their final match of the season condemned the club to demotion back to Division Three after just one season.