Nehlen served as the quarterbacks coach at the University of Michigan under Bo Schembechler from 1977 to 1979 before taking the head coaching job at West Virginia. Nehlen became West Virginia's 29th head football coach on December 7, 1979, replacing Frank Cignetti, who had posted four straight losing seasons. Nehlen first hired Gary Tranquill as the offensive coach. In an effort to emulate the Michigan defense, Nehlen hired Dennis Brown away from the Wolverines. Nehlen hired a number of coaches he worked with at Bowling Green. Nehlen also retained Donnie Young, Cignetti's former assistant head coach, as his recruiting coach. Tranquill left West Virginia after three seasons to become head coach at Navy, taking graduate assistant Steve Dunlap with him. Dunlap later returned to serve as West Virginia's defensive coach. One of Nehlen's most famed assistants was Doc Holliday, who served the assistant head coach and recruiting coach for almost 20 years before leaving for North Carolina State University. Holliday was sent to Florida every year to find recruits and found many talented players there, including linebackerSteve Grant. When Nehlen arrived at West Virginia, he introduced the Mountaineers' first "home and away uniforms" and a new helmet logo, "The Flying WV," which became the official logo of West Virginia athletics and, eventually, the university itself. In 1980, Nehlen's first season at West Virginia, the Mountaineers went 6–6. 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, 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. The 1987 season marked the beginning of the Major Harris era at West Virginia. In Harris' sophomore season, 1988, the Mountaineers went undefeated in the regular season and faced top-ranked Notre Dame in the Fiesta Bowl. Harris was injured on the third play of the game and West Virginia lost, 34–21. Notre Dame was crowned as national champions. 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. Nehlen's 1994 team started the season with a 1–4 record, but rebounded to qualify for the Carquest Bowl, where they lost to South Carolina, 24–21. In 1998, West Virginia featured a number of future National Football League 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. The Mountaineers opened the season with a home loss to Ohio State, but finished the season with an 8–4 record, losing in the Insight Bowl to Missouri, 34–31. Following a loss to Syracuse in 2000, Nehlen announced that the season would be his final one as head coach. On December 28, he coached his final game against Ole Miss in the Music City Bowl. 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. Nehlen completed his tenure at West Virginia with a record of 149–93–4. His 149 victories are the most in school history. With the Mountaineers, Nehlen coached 15 first team All-Americans, 82 All-Big East Conference honorees, and 80 future NFL players. In 1988, Nehlen was recognized with three national coaching awards, the Walter Camp Coach of the Year Award, the Bobby Dodd Coach of the Year Award, and the AFCA Coach of the Year. In 1993, he was named the Big East Coach of Year. Nehlen was inducted into the College Football Hall of Fame in 2005.