Gilbertson became the head coach at Washington in 2003 following the abrupt summer dismissal of Neuheisel. His first season was fairly respectable 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, including only their second winless PCC/Big Five/Pac-8/Pac-10 record in peacetime. He was fired near the end of the season; his record at Washington was , at the time the worst in the history of the program; it has since been surpassed by that of his successor, Tyrone Willingham. He then returned to the Seahawks as an assistant under Mike Holmgren.