Koetter was the head coach for three seasons at Boise State from 1998 to 2000, then moved to Arizona State in 2001. His record with the Broncos was 26–10 (.722), with two Big West Conference titles and two bowl victories and was named Big West Coach of the Year twice . At Arizona State, Koetter compiled a 40–34 (.541) record, and four Bowl appearances in six years. Under Koetter, who was also the offensive play caller, the Sun Devils became known for a vertical passing attack. On November 26, 2006, The Arizona Republic reported that Koetter was being terminated as ASU football coach. His final game was the 2006 Hawaii Bowl on Christmas Eve, a 41–24 loss.
In 2007, Koetter accepted the position of offensive coordinator for the Jacksonville Jaguars of the National Football League (NFL). In his first year in the NFL, he had immediate success setting franchise records for total points scored and yards gained while helping the Jaguars to a 11-5 record. In his five seasons with the Jaguars, the team cumulatively ranked third in the NFL in rushing yards over that time span in addition to having the NFL's leading rusher in Maurice Jones-Drew in 2010.
On January 15, 2012, Koetter was hired as the offensive coordinator for the Atlanta Falcons. On January 2, 2013, the Atlanta Falcons signed Koetter to a contract extension that ran through the 2014 season. Koetter was then hired by the Tampa Bay Buccaneers to become their offensive coordinator in 2015. After the firing of Lovie Smith, Koetter was hired on January 15, 2016 to become the Tampa Bay Buccaneers head coach.