Goodner was the linebackers coach at Baylor University from 1982 through 1991, becoming Baylor's defensive coordinator in 1992.
In 1993 Goodner left Baylor for Texas Tech University where he served as linebackers coach through 1994, becoming defensive coordinator there in 1995 under head coach Spike Dykes. Goodner was Texas Tech's defensive coordinator through the 1999 season, becoming the university's highest-paid assistant coach before his departure.[4]
In 2000 Goodner was hired as defensive coordinator at the University of Kentucky by head coach Hal Mumme. He was retained by the new head coach Guy Morriss for the 2001–2002 seasons, and joined Morriss as defensive coordinator at Baylor in 2003.