He was the head coach at the University of Northern Iowa, a position he held from 2001 until his retirement in 2024.

He led the team in tackles in 1984 and 1985, was named Gateway Football Conference Co-Defensive Player of the Year in 1985, first team all-conference three times, earned honorable mention All-America honors twice and twice named Academic All-American.

In 1997, he followed Allen to the University of Kansas, but left in 2001 when the head coaching position at his alma mater opened up.

In early 2008, Farley served as the interim director of athletics at Northern Iowa.

Farley notched his 150th Northern Iowa career win with a home victory over Southern Utah on September 7, 2019.