In his final year at Western Kentucky, he led the 2002 Hilltoppers to an NCAA Division I-AA Football Championship title.

In his junior year, the Falcons finished the season 9–0 and were named the small college division national champions.

After leaving Western Kentucky, Harbaugh served as an associate athletic director at Marquette University, Milwaukee, Wisconsin, where his son-in-law, Tom Crean, was the head coach of the men's basketball team.

Harbaugh retired in 2006, but served as Stanford's running backs coach in the 2009 Sun Bowl under his son, Jim.

Jack and Jackie settled in Mequon, Wisconsin, when he took the position as Associate Athletic Director for Marquette University in Milwaukee.

[10] Harbaugh is a member of the Bowling Green State University chapter of Phi Delta Theta fraternity.

They faced each other again in a second 'Har-bowl' when Baltimore beat San Francisco on February 3, 2013, at Super Bowl XLVII in New Orleans by a score of 34–31.

Their daughter Joani's husband, Tom Crean, has been the head men's basketball coach at Marquette, Indiana, and Georgia.