Hofher's coaching career began in 1981 as the quarterbacks and wide receivers coach at Miami of Ohio. Since then he's held offensive assistant coaching positions at Wake Forest, Syracuse, Tennessee, North Carolina and Bowling Green. He was the head coach at Cornell from 1990 to 1997 and at Buffalo from 2001 to 2005. In 1998, Hofher resigned at Cornell to join the staff at North Carolina. Hofher spent one year as quarterbacks coach for at Bowling Green State University in 2008 under head coach Gregg Brandon. He was hired in 2009 by Delaware to serve as their offensive coordinator and quarterbacks coach. During the 2011 off-season, Hofher was considered a candidate by Boston College for the offensive coordinator position, but was not hired. After four seasons with the Blue Hens, Hofher was released on November 18, 2012, after the team posted a 5−6 record in 2012. From 2016-2017, he served as the passing game coordinator and quarterbacks coach at the Iowa State University.