Before entering the NFL as a defensive quality control assistant with Green Bay in 1998, Flajole spent 21 years coaching in the college ranks. He served as Nevada's co-defensive coordinator/secondary coach for two seasons from 1996-1997. His 1996 defense finished first in the conference in total defense, scoring defense and passing defense. Prior to his duties at Nevada, Flajole held coaching positions at several other universities, beginning with his alma mater, Pacific Lutheran, from 1977–1978, and then Washington in 1979. Other stops included Montana from 1980–1985, Texas-El Paso from 1986–1988, Missouri from 1989–1993, Richmond in 1994 and Hawaii in 1995, holding defensive coordinator positions at Montana and Richmond.
Flajole replaced Sal Sunseri as linebackers coach for the Carolina Panthers in 2003, bringing with him five years of NFL coaching experience. He spent three seasons as defensive backs coach and one as linebackers coach with the Seattle Seahawks from 1999-2002 and one as a defensive assistant with the Green Bay Packers in 1998. As defensive backs coach for Seattle in 1999, Flajole's secondary led the NFL with 30 interceptions, including two that were returned for touchdowns. He spent the 2000 campaign as the Seahawks linebackers coach and returned to oversee the defensive backs in 2001 and 2002.