Huarte was drafted in 1965 by the American Football League's New York Jets and by the National Football League's Philadelphia Eagles. He signed with the Jets, but was beaten out for the starting position by fellow-rookie, Alabama's Joe Namath, who had finished the 1964 season 11th ranked in the Heisman voting. The AFL Jets thus signed both the Heisman Trophy winner and the Alabama star away from the NFL. Prior to the 1966 season he was traded by the Jets to the Boston Patriots for the draft rights to Wichita State University linebacker/center Jim Waskiewicz. Subsequently Huarte did see action as a back-up quarterback for several other professional teams from 1966-1972. He played his final two seasons of professional football as the starting quarterback of the Memphis Southmen of the World Football League.
Huarte is a member of The Pigskin Club Of Washington, D.C. National Intercollegiate All-American Football Players Honor Roll, and is also the founder and CEO of Arizona Tile Supply, Inc. In 2005 he was inducted into the College Football Hall of Fame.