Jurgensen was drafted in the fourth round of the 1957 NFL Draft by the Philadelphia Eagles. He was Philadelphia's backup quarterback, behind Bobby Thomason in 1957 and Norm Van Brocklin, from 1958 through 1960. It was during this time as a backup that Jurgensen was a part of a championship team for the only time in his professional career, when the Eagles won the 1960 NFL Championship, although Jurgensen did not appear in any postseason games.