The 1999 Appalachian State Mountaineers football team was an American football team that represented Appalachian State University as a member of the Southern Conference (SoCon) during the 1999 NCAA Division I-AA football season.
In their 11th year under head coach Jerry Moore, the Mountaineers compiled an overall record of 9–3, with a conference mark of 7–1, and finished as SoCon co-champion.
Appalachian State advanced to the NCAA Division I-AA Football Championship playoffs, where they were upset by Florida A&M in the first round.
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