At the conclusion of Stouffer's collegiate career, he gained notoriety when, after being selected by the St. Louis Cardinals in the first round (sixth overall) of the 1987 NFL draft, he sat out what would have been his rookie year due to a contract dispute.[3][4]
The following April, the Cardinals traded Stouffer's rights to the Seattle Seahawks for three draft picks,[5][6][7] who listed Stouffer as third-string behind starterDave Krieg and veteran backup Jeff Kemp in 1988. Krieg was sidelined in the third game with a separated shoulder,[8] and the following week Kemp was ineffective and was benched in favor of Stouffer by halftime. Stouffer endeared himself to Seattle fans in one play where, after stumbling and having his nose broken when it collided with a teammate's elbow, he threw for a long gain resulting in a touchdown against the San Francisco 49ers.[9] Stouffer filled in for nearly two months, until Krieg returned to the lineup in mid-November;[10] Seattle won the division (AFC West) with a 9–7 record, but lost in the divisional round of the AFC playoffs to top-seeded Cincinnati.[11][12][13] Stouffer seemed to regress in the eyes of Seahawk coaches over the next couple of years, and fell back to third string, behind Kemp.
Following the 1991 season, head coachChuck Knox was replaced by Tom Flores and Krieg was released. Stouffer won the starting job in 1992, ahead of Dan McGwire and Stan Gelbaugh. Stouffer was injured in week 5, as the Seahawks started the season 1–4. After McGwire was quickly injured, journeyman Gelbaugh became the starter, yielding the job to Stouffer once Stouffer recovered. Stouffer, who seemed to have been showing a return to his rookie form just before his injury, was never the same, however, and Gelbaugh quickly became the established starter.
The following season, Stouffer was released; he was signed by the Miami Dolphins to a free agent contract in April 1994 but was released prior to the regular season. Two years later, Stouffer was signed by the Carolina Panthers to a free agent contract in March 1996 but was released prior to the regular season.