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 a 67.2% of his passes (school record) for 2,365 yards and 11 touchdowns. He also set a school record with most consecutive passes completed (137) without an interception.
He left as the school's second career leader in passing yards with 4,603 passing yards, to go along with 436 completions (school record), 30 touchdowns, 342 rushing yards and a 23–6 record.
Pelluer was selected by the Dallas Cowboys in the fifth round (113th overall) of the 1984 NFL Draft. He was the third-string quarterback in his first two years. In 1985, with the first place in the NFC East division at stake, he was forced to enter a close game against the New York Giants and make his career debut, because both starting quarterback Danny White and backup Gary Hogeboom had been injured. Pelluer on his second series directed a 72-yard drive (which included a third-and-15 conversion) for the winning touchdown, leading the Cowboys to a victory that clinched the division title.
In 1986, he was named the backup quarterback after Hogeboom was traded. When White suffered a season-ending injury in week 9 against the New York Giants, Pelluer nearly rallied the team after completing 28-of-38 passes for 339 yards. He started 6 out of the last 7 games, showing a strong arm and great mobility. Against the Seattle Seahawks, he set the franchise record for consecutive passes completed (14) without an incompletion. He finished with a 1–6 record and was sacked 47 times in 9 starts.
In 1987, he began as a backup, but took over White in week 10 against the Miami Dolphins and started 4 out of the last 6 games. He finished with 94 straight passes without throwing an interception.
In 1988, at a low point in franchise history, he started 14 of the 16 games, passing for 3,139 yards, 17 touchdowns, rushing for 314 yards (second on the team) and 2 touchdowns, but the team finished just 3–13 (3–11 in his starts). In the seventh game against the Chicago Bears, while sliding feet first, a fierce hit by linebackerMike Singletary forced him to leave the game with a concussion.. In the eighth game against the Philadelphia Eagles, he completed 32 (second in team history) out of 46 passes for 342 yards. In the fifteenth game against the Washington Redskins, he passed for 333 yards and 3 touchdowns. He was the last quarterback to start and win a game for a Tom Landry-coached team and became one of only 3 quarterbacks in franchise history to pass for more than 3,000 yards in a season, joining Roger Staubach (2 times) and Danny White (4 times).
In 1989, he appeared in 5 regular season games with 3 starts. On November 5, he led his team to a 20–10 win against the Seattle Seahawks and tied a franchise record for rushing yards (69) by a quarterback.
In 1990, he appeared in 13 games with no starts, after Steve DeBerg established himself as the team starter during the preseason.
On August 7, 1991, he walked out of training camp, before returning on August 19. He was released on August 27 and later re-signed on December 17 to back up Mark Vlasic after DeBerg was injured.