After graduation, he joined the coaching staff at the University of Maryland in 1998 under head coach Ron Vanderlinden, who had been Fitzgerald's defensive coordinator during his playing days at Northwestern. He then moved on to the University of Colorado under his former Northwestern head coach, Gary Barnett. He took a job at the University of Idaho before returning to Northwestern in 2001, where he served as linebackers coach and recruiting coordinator until his promotion to head coach after the unexpected death of Randy Walker in June 2006. The Wildcats struggled in Fitzgerald's first season as head coach going only 4–8 overall and 2–6 in the Big Ten. The 'Cats improved to 6–6 the following year before going 9–3 in the 2008 regular season (5–3 in conference play) and playing in the Alamo Bowl. After the season, Fitzgerald was named the Big Ten Coach of the Year by the Touchdown Club of Columbus. The 2009 season saw the Wildcats go into Iowa City and knock off Iowa 17–10 on November 7. The win over Iowa came when the Hawkeyes were ranked #4 in the BCS standings and is, to date, the highest ranked opponent ever defeated by a Fitzgerald coached team. Two weeks later, the Wildcats knocked off #14 Wisconsin in Evanston for the second upset win of the season. Northwestern finished off the '09 campaign with a thrilling game in the 2010 Outback Bowl that saw Wildcat quarterback Mike Kafka set not only school records with 47 completions on 78 attempts for 532 passing yards but set all-time all-bowl records in those categories as well. The Wildcats fell 38–35 in overtime to Auburn (who would win the BCS Championship the following season) when a fake field goal attempt fell short. Nearly six million viewers watched the Wildcats play in their first New Year's Day bowl since 1996 in one of the most entertaining games of the 2009–2010 bowl season. The Wildcats' winning ways under Fitzgerald continued in 2010, highlighted by a dramatic last minute 21–17 upset of then #13 Iowa en route a third straight winning season and a third consecutive bowl game. In 2011, the Fitzgerald-led Wildcats defeated #9 Nebraska in Lincoln 28–27 with back-up quarterback Kain Colter guiding the Wildcats in the second half. Fitzgerald became only the second coach in school history to coach two nine-win Wildcat teams during the 2012 campaign that saw the 'Cats go 9–3 in the regular season and 5–3 in the Big Ten. Northwestern played in the third New Year's Day bowl game under Fitzgerald when the team accepted an invitation to play in the 2013 Gator Bowl.