| Year: | 1999 |
| Team: | Marshall Thundering Herd |
| Sport: | football |
| Conference: | Mid-American Conference |
| Division: | East Division |
| Short Conf: | MAC |
| Coachrank: | 10 |
| Aprank: | 10 |
| Record: | 13–0 |
| Conf Record: | 8–0 |
| Head Coach: | Bob Pruett |
| Hc Year: | 4th |
| Cooff Coach2: | Gunter Brewer |
| Cooc2 Year: | 4th |
| Cooff Coach1: | Marty Galbraith |
| Cooc1 Year: | 1st |
| Def Coach: | Tim Billings |
| Dc Year: | 1st |
| Stadium: | Marshall University Stadium |
| Champion: | MAC champion MAC East Division champion Motor City Bowl champion |
| Conf Champ: | MAC Championship Game |
| Conf Champ Result: | W 34–30 vs. Western Michigan |
| Bowl: | Motor City Bowl |
| Bowl Result: | W 21–3 vs. BYU |
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.
Marshall outscored its opponents 463–137 en route to an undefeated, 13–0, season. The season-opener at Clemson (13–10) and the MAC Championship Game vs. Western Michigan (34–30) were the only games decided by less than 12 points.
See also: 1999 Clemson Tigers football team.
See also: 1999 Liberty Flames football team.
See also: 1999 Bowling Green Falcons football team.
See also: 1999 Temple Owls football team.
See also: 1999 Miami RedHawks football team.
See also: 1999 Toledo Rockets football team.
See also: 1999 Buffalo Bulls football team.
See also: 1999 Northern Illinois Huskies football team.
See also: 1999 Kent State Golden Flashes football team.
See also: 1999 Western Michigan Broncos football team.
See also: 1999 Ohio Bobcats football team and Battle for the Bell (Marshall–Ohio).
See also: 1999 Western Michigan Broncos football team and 1999 MAC Championship Game.
See also: 1999 BYU Cougars football team and 1999 Motor City Bowl.
The following players were selected in the 2000 NFL draft.
| Player | Position | Round | Pick | Franchise |
| Quarterback | 1 | 17 | New York Jets | |
| Defensive Back | 2 | 43 | San Diego Chargers | |
| Running Back | 3 | 88 | Minnesota Vikings | |
| Wide Receiver | 6 | 175 | Seattle Seahawks | |
See also: 1999 NCAA Division I-A football rankings.