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The university charter was signed 1991, but students did not begin attending classes until 1997. The athletic programs began as members of the NAIA. The school hired Karl Smesko while the school was still in the NAIA, but his first year coincided with the transfer to NCAA Division II in 2002. In his first year, the basketball facilities were not yet completed at the beginning of the season, so players began individual workouts on outdoor courts. His first office was in a trailer. Despite having no experience as a team, the Eagles opened their season against Ohio Dominican and won. Then they won their next game, and the next, and continued winning until they faced St. Francis of Indiana, who beat the Eagles to give them their first loss. That would be the last loss of the season, as they went on to a thirty win season, with a 30–1 record.

The team continued to pile up winning records, and went on to post a 29–2 record in and earn an invitation to the DII post-season tournament in 2006. The team would advance as far as the Regional semi-final. After reaching a national DII ranking of eleven, the team faced ninth ranked Rollins, and won 48–46. The team then faced seventh ranked Delta State who ended the Eagles season with a 57–48 win.

FGCU then joined the Atlantic Sun Conference, although they would be provisional members until 2011. The finished in second place in the conference in both 2008, and 2010. The 2009 team did finish first in the conference during the regular season but due to the transition to Division I and the Atlantic Sun Conference, was not eligible for conference or NCAA Tournament play. The team earned invitations to the post-season WNIT tournament, advancing to the second round in 2008 and 2009. In 2011, the team would go 28–4 overall, with a 17–3 record in conference. That record was the best in conference, resulting in the first regular season conference title for the Eagles. The team would not become a full member of the conference until August of that year, so was not part of the conference post-season tournament. They did participate in the 2011 WNIT, beating Drexel in the first round before losing to Florida in the second round.

In 2012, their first year of eligibility for the Atlantic Sun post-season tournament, they went undefeated in conference play, with an 18–0 as part of an overall 29–3 record. They won the conference tournament, earning a bid to the NCAA tournament. They took on St. Bonaventure in their first NCAA game and took the Bonnies to overtime, before succumbing 72–65.

The following year, the team also went undefeated in regular season conference play, but ended up with a loss to Stetson in the conference championship game. Although the team had lost eight players from the year before, they had won all their conference games by double digits. They held a double-digit lead in the conference final, but then went on a long scoreless streak, allowing the Hatters to get back into the game and win, 70–64. The Eagles earned an invitation to the WNIT but lost in the first round.

2012 Paradise Jam

FGCU participated at the Paradise Jam in St. Thomas. The four teams invited to the Reef Division of tournament were:

• DePaul University
• Florida Gulf Coast University
• Hampton University
• University of South Carolina

The teams played in a round-robin format over the Thanksgiving weekend. In their game against DePaul, the Eagles fell behind early, down as much as 12 points in the first half. They came back to cut the deficit to a single point at halftime. After taking a brief, one-point lead early in the second half, the Blue Demons took back the lead, and extended it to nine points with under eight minutes to go. The lead was still eight points with just over two minutes left, when Taylor Gradinjan was fouled on a three-point attempt, and hit all three free throws. Katie Meador hit a basket with 23 seconds remaining, and Sarah Hansen scored with eight seconds left, but DePaul held on for a two-point victory.

2013 Academic award

In the 2012–13 season, the team achieved a GPA of 3.621, which was high enough to be in fourth place among Division I teams, and earned a position on the WBCA Academic honor roll.