At the conclusion of his collegiate career, he achieved notoriety when, after being selected by the St. Louis Cardinals in the first round of the 1987 NFL Draft, he sat out what would have been his rookie year due to an inability to agree on a contract. The following season, the Cardinals traded his rights to the Seattle Seahawks, who listed Stouffer as third-string behind starterDave Krieg and veteran backup Jeff Kemp. Krieg would be sidelined with a separated shoulder, and the following week Kemp was ineffective starting in place of Krieg and was benched in favor of Stouffer by halftime. Stouffer endeared himself to Seattle fans in one play where, after having his nose broken, he threw for a long gain resulting in a touchdown. For several weeks, Stouffer filled in until Krieg returned to the lineup. Stouffer seemed to regress in the eyes of Seahawk coaches over the next couple of years, and fell back to third string behind Kemp.
Once Seahawk head coachChuck Knox was replaced by Tom Flores and Dave Krieg was let go, Stouffer won the starting job, beating out Dan McGwire and Stan Gelbaugh. Stouffer was injured in week 5, and 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.
Stouffer 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.