Duggan served as the head coach for the Cologne Centurions of NFL Europe from 2006 to 2007, where he compiled a record of 10–9.
During his one year stay with the Gators, they won the North Coast Athletic Conference title and participated in the NCAA Division III playoffs.
In his final year at UNH, the Wildcats won the Yankee Conference title and participated in the NCAA Division I-AA playoffs.
Duggan was fired on October 16, 2020, less than 24 hours after the Red Wolves defense gave up 52 points against Georgia State.
[4] In late December 2022, Duggan was named the defensive coordinator at Kent State under brand-new head coach Kenni Burns.