After the WLAF season finished, he was re-signed by the Dolphins on June 2, 1992. Pederson spent 1992 training camp with the Dolphins, before being released during final roster cuts again. He was subsequently re-signed to the team's practice squad, where he practiced on the scout team until he was waived on October 8, 1992. He was re-signed by the Dolphins after the season on March 3, 1993. After his third training camp with the Dolphins, he was waived again on August 31, 1993. For the second consecutive season, Pederson was re-signed to the team's practice squad, on September 1, 1993. Dan Marino, the Dolphins' starting quarterback since 1983, ruptured his Achilles' tendon in a week 6 game against the Cleveland Browns on October 10, 1993, forcing backup Scott Mitchell to replace him. Pederson replaced Marino on the active roster, and served as Mitchell's backup for the next four games. Pederson made his NFL debut on October 24, 1993, in a week 8 game against the Indianapolis Colts. He helped head coach Don Shula win his NFL-record 325th victory as a coach when Mitchell suffered a separated shoulder in a week 11 game against the Philadelphia Eagles on November 14, 1993. In that record breaking game for Coach Shula, Pederson entered in the 3rd quarter of the game and went 3 for 6 for 34 yards, and completed several crucial 3rd downs. Pederson was able to steer the Dolphins to the win. Pederson also served as the backup to recently acquired Steve DeBerg for the three games Mitchell missed with injury. He briefly entered a week 14 game against the New York Giants while DeBerg was receiving stitches on his face. Mitchell returned as the Dolphins' starter after week 15, and Pederson was released in favor of backup DeBerg and third-string quarterback Hugh Millen on December 16, 1993. Pederson re-signed with the Dolphins on April 16, 1994, after the season ended. He spent the entire 1994 season on the Dolphins' active roster as the third-string quarterback behind Marino and Bernie Kosar. On February 15, 1995, Pederson was selected by the Carolina Panthers in the twenty-second round of the NFL Expansion Draft, after being placed on the Dolphins' available players list on January 19, but was released on May 24, 1995. He returned to the World League after his release, playing with Rhein Fire. Pederson re-signed with the Dolphins again in June 1995. After competing with Dan McGwire throughout training camp, Pederson was waived on August 22, 1995. Marino suffered a knee injury during a week 6 game, so Pederson was re-signed on October 10 to serve as the third quarterback behind Kosar and McGwire for the next two games. He was released again after Marino returned for week 9 on October 24.