Fisher played a season in the Arena Football League in 1988 for the Chicago Bruisers, then rejoined Terry Bowden at Samford as a graduate assistant coach working with quarterbacks from 1988–1990. He was subsequently hired as the full-time offensive coordinator and quarterbacks coach. After two seasons, Fisher moved with Bowden to Auburn University where he coached quarterbacks. At Auburn, Fisher coached several successful quarterbacks including Patrick Nix. He continued at Auburn until Tommy Tuberville took over as head coach following Terry Bowden's 1998 mid-season resignation.