The 1999 Marshall Thundering Herd football team represented Marshall University in the 1999 NCAA Division I-A football season. The Thundering Herd played their home games at Marshall University Stadium in Huntington, West Virginia, and competed in the East Division of the Mid-American Conference (MAC). The team was coached by fourth-year head coach Bob Pruett. Marshall became the second non-automatic qualifying team in the Bowl Championship Series (BCS) era to finish the year ranked in the top 10 of the AP Poll.