The Citadel jumped on Appalachian State early, scoring 38 points in the first half en route to a 52-28 victory on Saturday.
The Citadel moves to 3-0 overall and 2-0 in the Southern Conference for the first time since its championship season of 1992.
The Mountaineers (1-2) had won 17 of the past 18 games against the Bulldogs, including eight in a row.
Appalachian State's 18-game regular-season home winning streak was snapped.
The Bulldogs rushed for 463 yards and threw for 155 on 4-of-6 passing, rolling up 618 total yards. They held the ball for 38 minutes, 11 seconds.
Three Bulldogs rushed for more than 100 yards, with Ben Dupree racking up 180 yards and two TDs, Darien Robinson 113 and one score and Rickey Anderson 102 and a TD. Matt Johnson caught three passes for 123 yards.
Steven Miller rushed for 167 yards and three TDs for Appalachian State.