In his senior season, he returned to the offensive line, earning All-Big-Eight honors while helping Tom Osborne's 1978 team to a league championship.

[1] Cotton was a third-round pick in the 1979 NFL draft and played for one season with the Cincinnati Bengals before moving to the St Louis Cardinals.

In 1997, former Nebraska Cornhuskers player and New Mexico State University head coach Tony Samuel hired Cotton to the same position he had held at St.

Although championships eluded New Mexico State during Cotton's six years with the program, the production of his offensive players generated impressive statistics.

Despite helping Nebraska to a national top ten rushing offense and mentoring four linemen to earn All-Big 12 Conference honors, Cotton was let go along with nearly all of the other assistants after Solich was replaced by Bill Callahan following the 2003 season.

On November 30, 2014, two days after the Cornhuskers defeated the Iowa Hawkeyes 37–34 to finish the regular season with a 9–3 record, Cotton was appointed interim head coach for the upcoming bowl game, following the dismissal of Pelini.

[4] Jake played as an offensive lineman from 2010 to 2014, and signed pre-season free agent contracts the Houston Texans and the Ottawa Redblacks but did not make the final roster for either team.