They were members of the Eastern Indoor Soccer League and played only during the 1998 season.

The team suspended operations after the 1998 season, as did the Huntsville Fire, ultimately leading to the official collapse of the league in December 1998.

[12][13] The Pensacola Flyers finished sixth overall in the seven-team league, ahead of only the Savannah Rug Ratz.

[15] Pensacola Flyers forward Brad Snyder was named to the 1998 EISL All-League Third Team.

Players receiving All-League Honorable Mentions included midfielders Oleg Baleev and Diego Maradona.