In 2001 the Southeastern Association of Professional Baseball brought the sport back to Pensacola. In middle of the 2002 season, Quint and Rishy Studer bought the Pelicans franchise from the league. The Studers’ wanted to make this pastime a fun experience for fans. They instituted giveaways and donated a percentage of proceeds to charity. The Pelicans had a very successful regular season and earned the top spot in the playoffs. The Pelicans beat the Montgomery Wings in an extra innings victory to win the league championship at home. In 2002, the team had the highest attendance of the entire league

In 2003 the Pelicans started their season strong by winning their season opener against the Houma Hawks. Team captain and shortstop, Heath Kelly, was signed to play affiliated ball for the Tampa Bay Devil Rays midway through the season. The Pelicans went on to become the SEPBL regular season champions. The Pelicans swept the Macon Peaches in the playoffs 2-0 and went on to play the Baton Rouge Riverbats for the championship series. The Pelicans were defeated by the Riverbats and lost the series 3-1.

In 2004, the Pelicans joined the much established Central Baseball League (CBL). The CBL, formally the Texas-Louisiana League, is made up of eight teams: Jackson Senators, Shreveport Sports, Fort Worth Cats, Edinburg Roadrunners, El Paso Diablos, San Angelo Colts, Coastal Bend Aviators and the Pensacola Pelicans. The Pelicans impressed a lot of people and had a great first year in the league. Pensacola had a rocky start, going 4-12 but then won a team record 19 straight games, propelling them to first place. They finished second in the first half and won the CBL East Division Second Half Championship. The Pelicans, however, lost in the first round of the Playoffs to the East Division rival Shreveport Sports three games to two. Over the course of the season, four players were purchased by a major league organization, five players were either CBL Batter or Pitcher of the Week, pitcher Byron Batson was July's CBL Player of the Month and centerfielder Rafael Alvarez was named the CBL 2004 Player of the Year.

In 2005, the Pelicans enjoyed another successful season in the CBL ending with the second best record in the league (53-40). Despite having the second best record in the league, the Pelicans had to play the league’s best team, the Fort Worth Cats. Fort Worth was able to pull out the game five victory to win the series 3-2. Fort Worth would go on to win the CBL Championship. At the beginning of the season, Pelicans stand out first baseman Mario Valdez left the Pelicans to play in the highly touted triple "A" Mexican League. The other player to move up to a Major League organization was Edwar Ramirez when he was signed to a two year contract with the triple "A" team of the Los Angeles Angels. Besides the success on the field, there was also a great increase in attendance of a nearly 65% raise from 2004. In the off season, the Pelicans were busy making moves as they joined the newly developed American Association of Independent Professional Baseball. 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.

2006 was another breakout year for the Pelicans organization. The team broke several attendance records including a record crowd of more than 4,200 fans at the last game of the season. On July 4, 3,326 fans were in attendance for the 4th of July fireworks display and broke the old record of 3,113 fans set on August 14, 2004. The single game record was later shattered as 4,209 fans watched the Pelicans in the first-ever "Pack the Track Night" in which fans were able to sit on the warning track during the game. 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. The Pelicans saw had four players and three coaches sign with a major league team during 2006. Gerardo Casadiego (P) signed with the New York Yankees, Clint Sodowski (P) signed with the Atlanta Braves, Carlos Mendoza (SS) signed with the New York Yankees, and Tony Pierece (P) signed with the Braves. Coach Craig Bjornson signed with the Seattle Mariners, George Hernandez signed with the Florida Marlins and former player Joe Espada is now coaching in the Marlins organization. On the field, the Pels experienced their first losing season since their inception, finishing with a record of 39-57. Off the field, the biggest milestone in Pensacola baseball history was passed in the Vince Whibbs Community Maritime Park. The Park features a multi-purpose stadium which will be the home of the Pelicans, UWF classrooms and conference center and a maritime muesum. The Pelicans are expected to play their first game in 2009.

At the beginning of 2007, the Pelicans found a new home on Davis Highway in Pensacola. In addition to the new office, the Pelicans opened the Pelicans Training Academy, a 12,000 square foot in-door baseball and softball training facility. The building features nine batting cages, pitching mounds, three Iron Mike pitching machines, and a pro shop. Full time instructors hold various camps, clinics, and individual or group lessons. Pelicans new Field Manager, Mac Seibert, heads up the Academy during the off-season. Seibert joined the Pelicans after an extensive history in scouting, which included being the National Cross Checker for the Tampa Bay Devil Rays. In the stands, the Pelicans continued to break franchise records. On May 27, Tracey Pingel walked through the gates as the Pelicans 250,000 fan since their inception. With the 2007 season, all-time attendance now sits at 322,553. On June 24, the Pelicans had an overflow crowd of 6,238 enter the park. Safe at Home Ministries held a post-game Christian concert featuring Big Daddy Weave and Mandisa to draw the single game record crowd. Again, the Pelicans upped their average game attendance to 1,967. One day prior to opening day, the Houston Astros purchased the contract of the Pelicans number one starter Kyle Middleton. The big right-hander became the Pelicans 17th player to be purchased by a MLB team. Also in 2007, the first Pelican made his debut in the Major Leagues. Right-handed pitcher Edwar Ramirez made his Major League debut with the New York Yankees on July 3 against the Minnesota Twins. In the 9th inning, he struck out the side to finish the game for the Yankees. At Pelican Park, the Pelicans began a relationship with the United States Marine Corps in which the Marines provided game day staff for 48 Pelicans home games. In return, the Pelicans compensated the Marines over $22,000 to help fund 5 Marine Corps Birthday Balls and recreational equipment for bachelor housing. On the lighter, promotional side of the sport, the Pelicans’ T.P. Tribute Night was named Promotion of the Year by GameOps.com. On the field, the Pels had their second consecutive losing season, finishing 39-56. Trino Aguilar (3B) was named to the mid-season and post-season all-star teams and Marcos Rodriguez (OF) was selected for the mid-season team. Cesar Aranguren was named the league Rookie of the Year.