In 1990, he accepted a position under Lou Holtz at the University of Notre Dame as assistant head coach and defensive coordinator. Darnell was replacing Barry Alvarez, who left to take the head coaching job at Wisconsin. He later joined John Mackovic's staff at the University of Texas at Austin as assistant head coach and special teams coordinator in 1992. Two years later, he moved from special teams to defensive coordinator, serving in that position through the 1996 season. He then moved on to become Western Michigan University's head coach in 1997.