Andersen began his football career playing at Cottonwood High School where he lettered in football for two years. After high school, he played center at Ricks College in Rexburg, Idaho, for two seasons. As a freshman he was second team All-Conference and Ricks finished the season ranked fourth in the nation. In 1984, he was a First Team All-America selection and team captain as he helped Ricks to a number two ranking in the nation. He transferred to the University of Utah in Salt Lake City, where he lettered two years for the Utes and graduated in 1986 with a bachelor's degree in political science.
Andersen was the head coach at Utah State for four seasons, beginning with 4–8 records in 2009 and 2010. His first winning season at Utah State came in 2011 and his fourth and final year was the most successful, as the 2012 Aggies won 11 games and lost only two, and finished #16 in the final AP poll.
Wisconsin
Andersen was introduced as the new head coach at Wisconsin on December 21, 2012 to replace Bret Bielema, who left for Arkansas. After Andersen decided to leave Utah State for the Wisconsin job, he called every one of his players at Utah State individually to inform them personally of his decision. In 2013, Andersen's first win as a Wisconsin coach was a 45–0 win against Massachusetts. Andersen's final 2013 record was 9–4. The 2014 regular season ended with the Badgers taking 1st place in the West division with a 10–2 record. Wisconsin played Ohio State for the conference title in the 2014 Big Ten Championship Game where the Badgers lost to Ohio State 59–0. Andersen left Wisconsin four days later, having taken the vacant head coaching position at Oregon State. Andersen cited family as his rationale for taking the Oregon State position while it was reported by some media outlets, such as Fox Sports and Sports Illustrated, that Andersen was frustrated with Wisconsin's high admissions standards for athletes. Those reports turned out to be accurate, and were confirmed by Andersen in January 2015. Andersen had to pay a $3 million buyout for departing within the first two years of his contract, which was set through January 2019.
Oregon State
Andersen was announced as the new head coach of Oregon State on December 10, 2014. Andersen replaced the previous coach at Oregon State, Mike Riley, who left for the same position at Nebraska. On October 9, 2017, Andersen and Oregon State football parted ways with him forgoing $12 million left on his contract.
Return to Utah
On January 2, 2018 it was announced that Andersen will be returning to Utah for a 3rd time as an associate head coach and defensive assistant.
Second stint at Utah State
On December 9, 2018, Andersen was named head coach at Utah State for the second time, replacing the man who replaced him six years earlier in Matt Wells, who left for the Texas Tech head coaching job.
