After 21 years in the Southwest Conference, the Cougars joined Conference USA in 1996. Under head coach Alvin Brooks, the basketball program had a disappointing initial season in C-USA. The team went 3–11 against C-USA teams in 1996–97. The next season was even more futile. Brooks, who had led the Cougars since 1993, coached the Cougars to a rock bottom conference record of 2–14 in 1997–98. The last, and only other, time the Cougars recorded only two conference victories in a season was in 1950–51; their first season in the Missouri Valley Conference.