In 1996, the Charlotte 49ers men's soccer team became the first Conference USA team in any sport to reach the National semi-finals. The Niners won a school record 19 games. They went 7–1 in Conference USA to capture the regular season title. The Niners defeated College of Charleston, Notre Dame and Hartford to reach the national semi-finals before falling to Florida International in front of 20,269 fans in Richmond, Virginia. Goalkeeper Jon Busch becomes the Niners' second first team All-American after recording 12 shutouts and a 0.89 goals against average. Busch also earned Conference USA Defensive Player of the Year honors. John Tart was named Conference USA Coach of the Year.
The most notable season in Charlotte soccer history came in 2011 when the 49ers became the first team of any sport in school history to reach an NCAA national championship. The team was ranked in the top 25 throughout the entire season thanks to a challenging yet successful non-conference campaign. The Niners finished the regular season with an Atlantic 10 record of 6–1–2 and 13–3–2 record overall. After an early disappointing loss to Xavier in the Atlantic 10 tournament, Charlotte then went on a deep run in the NCAA Tournament. The unseeded Niners defeated Furman, No. 11 UAB, No. 10 Akron, and No. 5 Connecticut to advance to the program's second ever College Cup in Hoover, Alabama. The Niners went on to defeat No. 3 Creighton before falling to No. 1 North Carolina in the national championship game with a score of 1–0.