On March 19, 2007, Paup was introduced as the head football coach at Green Bay Southwest High School. He compiled a 22-14 regular season record in his first four seasons, and in 2009 secured the second playoff victory in school history. He is also on the Packers' Board of Directors. Prior to accepting the job, he was an assistant volunteer football coach for the De Pere High School Redbirds of De Pere, Wisconsin for three years, working primarily with the linemen and linebackers.
On March 5, 2013, Paup resigned at Green Bay Southwest and is entering his first season as the defensive line coach at the University of Northern Iowa.
Paup lives in Cedar Falls, IA, with his wife Denise. They have six children: Alex, Nathan, Rachel, Hailey, and twins Paige and Lauren.