In 2017 the AFCA presented Nehlen the Amos Alonzo Stagg Award, given to the "individual, group or institution whose services have been outstanding in the advancement of the best interests of football.

Nehlen became West Virginia's 29th head football coach on December 7, 1979, replacing Frank Cignetti, who had posted four straight losing seasons.

Tranquill left West Virginia after three seasons to become head coach at Navy, taking graduate assistant Steve Dunlap with him.

In 1981, led by quarterback and future WVU athletic director Oliver Luck, West Virginia went 9–3 and upset the Florida Gators in the Peach Bowl, 26–6.

In 1982, led by quarterback Jeff Hostetler (who ended up marrying Nehlen's daughter, Vicky), West Virginia started the season with an upset over the #9 Oklahoma Sooners.

In 1984, Nehlen's squad posted wins against Boston College, led by eventual Heisman Trophy winner, Doug Flutie, and over Penn State for the Mountaineers' first defeat of the Nittany Lions since 1955.

In 1993, Nehlen led West Virginia to another undefeated regular season and a Big East Conference title, but the Florida Gators exacted revenge in the Sugar Bowl, winning 41–7.

In 1998, West Virginia featured a number of future National Football League (NFL) players including Marc Bulger, Amos Zereoué, Anthony Becht, Gary Stills, Barrett Green, Solomon Page and John Thornton, to form a strong nucleus on a team that lacked depth on defense.

After winning three of their first four bowl games, Nehlen's West Virginia teams had lost eight straight postseason contests, but his final squad, led by the offensive attack of quarterback Brad Lewis, tailback Avon Cobourne, wide receiver Antonio Brown, and fullback Wes Ours, handled the Rebels, 49–38.