Stewart served as an assistant on the Mountaineers coaching staff beginning in 2000. He coached in that capacity until December 2007, when then West Virginia head coach Rich Rodriguez left for Michigan. At that point, Stewart took over as the school's interim head coach, eventually becoming the full-time head coach after the Mountaineers' Fiesta Bowl victory.
Stewart went 28-12 in three seasons as head coach before being replaced prior to the 2011 season. He failed to earn a BCS berth in that time.
