After three stints as a graduate assistant, Gilbertson became an offensive coordinator in 1977 at Utah State under head coach Bruce Snyder. After five seasons in Logan, he joined Dennis Erickson's new staff at Idaho, who immediately turned the Vandal program around in 1982, going 8–3 in the regular season and advancing to the quarterfinals of the I-AA playoffs. Shortly after, Gilbertson departed for the Los Angeles Express of the newly-formed United States Football League (USFL), where he coached as offensive coordinator for three spring seasons. Following the demise of the league, Gilbertson returned to Idaho in 1985, and the Vandals won their first Big Sky Conference title in fourteen years.
Erickson departed for Wyoming in December,[2] and Gilbertson was promoted to head coach of the Vandal program.[3] In his three seasons in Moscow as head coach (1986–88), Gilbertson's win–loss record was 28–9 (.757), which remains the best in UI history.[4] His 19–4 (.826) record in conference play was the best-ever in the Big Sky.[5]
Two weeks after winning the Rose Bowl, Gilbertson became the head coach at California in January 1992.[12] Despite leading Cal to a 9–4 record in 1993 with a decisive victory in the Alamo Bowl, he was dismissed after his fourth season when the 1995 Bears went 3–8. Gilbertson's overall record at Cal was 20–26 (.435).[13]
After Cal, he was an assistant coach for the Seattle Seahawks of the National Football League (NFL) for three seasons (1996–98) under Erickson; the last two years as tight ends coach. In 1999, he returned to the Washington Huskies as an assistant head coach under new head coach Rick Neuheisel.
Gilbertson became the head coach at Washington in 2003, following the abrupt summer dismissal of Neuheisel. His first season ended at 6–6; only a blowout loss to Cal in the next-to-last game of the season kept the Huskies out of a bowl game. The bottom fell out a year later, in which the Huskies finished 1–10. He resigned prior to the end of the season but remained the head coach through their last games; his record at Washington was 7–16 (.304) [14] He then returned to the Seahawks as an assistant under Mike Holmgren.
Gilbertson's overall record as a collegiate head coach is 55–51 (.519).