Seely made the jump to the professional level in 1989, working as the tight ends and special teams coach for the Indianapolis Colts through 1993. He then spent the 1994 season with the New York Jets as their special teams coach. In 1995, Seely began a 4-year stint with the Carolina Panthers also as their special teams coach, winning the NFL Special Teams Coach of the Year Award in 1996. He joined the Patriots on January 27, 1999. Following 10 seasons with the Patriots as their special teams coach under Pete Carroll and Bill Belichick, Seely joined former Patriots assistant Eric Mangini's coaching staff in Cleveland as their assistant head coach and special teams coach in 2009. Beginning in 2011, he is Special Teams Coordinator and Assistant Head Coach with the San Francisco 49ers. He was hired by the Raiders on January 20, 2015.