The Pensacola Pelicans were incorporated in 2001, when the Southeastern League decided to place a team in the Pensacola area. Midway through the 2002 season, Quint and Rishy Studer bought the team from the league. The 2002 was a very successful season for the Pelicans; they had the league's best record and won the championship in an extra-innings victory against the Montgomery Wings. The 2003 season was also successful, with the Pelicans once again claiming the league's best record, but losing to the Baton Rouge Riverbats in the championship series.
Before the 2004 season, the Orlando Rays of the Southern League moved to Montgomery, Alabama, the location of a key Southeastern League franchise. Unable to compete with an affiliated baseball club in one of its key cities, the Southeastern League folded, and the Pelicans were left without a league in which to play.
The Pelicans were defeated by the Riverbats and lost the series 3-1.
Five teams from the CBL (Pensacola, Fort Worth, Shreveport, Coastal Bend and El Paso) joined with four teams from the Northern League (Sioux City, Sioux Falls, St. Paul and Lincoln) and one new team (St. Joseph) to form the new "super" independent league.
In 2006, the Pelicans also raised their average attendance to 1,641 as a new season attendance record of 78,755 fans watched a game during the season.