He went on to play at the University of Washington. As a sophomore in 1981, he took over the starting quarterback position, after Tim Cowan injured his thumb in the second game of the season. He finished with 110 of 234 completions, for 1,138 yards and 9 touchdowns, while leading the team to a Pacific-10 Conference title and a 28-0 win over the University of Iowa in the 1982 Rose Bowl. In 1982 even though his record was 7-1, he lost his starting job to Cowan. In 1983 he had one of the best quarterback seasons in school history, receiving All-Pac-10 and the conference's offensive player of the year honors, after completing 213 of 317 (.672 avg.) passes, for 2,212 yards and 11 touchdowns.
He left as the school's second career leader in passing yards, while compiling a 26-7 record.
In 1986 he was the backup quarterback after Hogeboom was traded, and when White suffered a season-ending injury in week 9, he became the starter for the remainder of the season, showing a strong arm and great mobility. Playing against the Seattle Seahawks, he set the franchise record for consecutive passes completed (14) without an incompletion.
In 1987 he was White's backup, but took the starting job in week 10. In 1988 at a low point in franchise history, he started 14 of the 16 games, passing for 3,139 yards and 17 touchdowns, but the team finished just 3-13 (3-11 in his starts). That year against the Chicago Bears, while sliding feet first, he received a highlight-reel hit by linebackerMike Singletary, that forced him to leave the game with a concussion. He was the last quarterback to start and win a game for a Tom Landry-coached team.
In 1989, the Kansas City Chiefs sent a third round draft choice in 1990 and a fourth round draft choice in 1991 to the Dallas Cowboys in exchange for Pelluer. He was a member of the team for two years and started only three games.