Van Pelt was an eighth round draft pick of his hometown Pittsburgh Steelers, but was released during training camp. Van Pelt spent three games with the Kansas City Chiefs late in the 1993 NFL season following a hamstring injury to Joe Montana. He was re-signed by the Chiefs prior to the 1994 NFL season, but was released during training camp. He was signed by the Buffalo Bills later in the 1994 season following a knee injury sustained by Jim Kelly and spent the remainder of his career as a backup with the Bills.
Van Pelt's first NFL win as a starter would come on November 2, 1997, against Dan Marino and the Miami Dolphins. In 2001, he started 8 games, going 2-6, and playing well enough to justify a contract extension that would allow the Bills to release failed Doug Flutie successor Rob Johnson. Van Pelt would not start any games after 2001 due to a Bills trade with the New England Patriots for Drew Bledsoe, who became the full-time starting quarterback. Van Pelt remained with the team as Bledsoe's backup for the next two seasons before retiring.
In his eleven-year career, Van Pelt totaled 16 touchdowns and 24 interceptions on 477 pass attempts in 31 career appearances and 11 starts.
Van Pelt was hired by the Tampa Bay Buccaneers as the quarterbacks coach on February 1, 2010. When Buccaneers head coach Raheem Morris was fired on January 2, 2012, the whole staff was let go as well.