Marshall left the Southern Conference and Division I-AA after the 1996-97 academic year. In 1997, the Thundering Herd joined the Division I-A Mid-American Conference, of which it had been a member nearly three decades before.
Marshall competed for eight years in the MAC, winning five bowl championships and six conference titles. Perhaps its most memorable football season was in 1999, when Marshall went 13-0, defeated traditional national powers Clemson 13-10 in the season opener and Brigham Young 21-3 in the Motor City Bowl, and earned a top 10 national ranking. Other signature victories for Marshall during its years in the MAC came against South Carolina, 24-21, in 1998, and against then sixth-ranked Kansas State, 27-20, in 2003.
Marshall won more football games than any other Division I-A or I-AA team in the 1990s, going 114-25. From 1996 through 1999, the Herd was an incredible 50-4 – a winning percentage of .926. Since 1991, the Thundering Herd has played its home games at Marshall Stadium – later renamed Joan C. Edwards Stadium, which has expanded to a capacity of more than 38,000.