Augusta made their first NCAA Tournament appearance after capturing their first Peach Belt Conference North Division title in 2003. The Jaguars earned the No. 6 seed and fell 68-59 to Columbus State in the first round of the NCAA South Atlantic Regional.
Augusta returned to the NCAA South Atlantic Regional in 2004 as the eighth seed and won the tournament to advance to their first and only Elite Eight appearance. The Jaguars beat Shaw 81-64 in the opening round, beat Armstrong 79-74 in the semifinals, and rolled Georgia College 91-68 in the championship game. Merrimack won 76-68 over Augusta in the first round of the Elite Eight.
The Jaguars earned an at-large bid to the NCAA South Atlantic Regional as the fifth seed and upset Shaw for the second-straight season with an 88-70 win. In the regional semifinal game, Wingate outlasted Augusta 66-65 on a last minute put-back bucket.
Augusta drew the eighth seed in the NCAA Southeast Regional. Making their fourth NCAA Tournament appearance, the Jaguars upset the top-seeded and previously undefeated No. 2 nationally-ranked Limestone Saints 79-70 in the first round. In the semifinal game, Augusta rallied against Anderson and won 81-73, before Francis Marion prevailed 72-65 in the Sweet 16.