The 1999 James Madison Dukes football team represented James Madison University (JMU) during the 1999 NCAA Division I-AA football season. It was the program's 28th season and they finished as Atlantic 10 Conference (A-10) co-champions with UMass after posting a 7–1 record in conference play. The Dukes earned a berth as the #12 seed into the 16-team Division I-AA playoffs, but lost in the first round to #5 seed Troy State, 7–27. JMU was led by first-year head coach Mickey Matthews.