On December 1, 2004,
Notre Dame defensive coordinator Baer was named interim head coach after regular head coach
Tyrone Willingham was fired. Notre Dame eventually hired
Charlie Weis as new head coach starting 2005. Baer was a 2002 finalist for the
Broyles Award, given annually to the nation's top college football assistant coach. However, the Fighting Irish gave up 26.4 points per game in Baer's final 26 games on the coaching staff, from the 12th game of the
2002 season through the end of the
2004 season. On January 3, 2005, after Willingham became head coach at
Washington, Baer joined Willingham's staff as defensive coordinator. At the conclusion of the 2007 season, after a statistically worst defensive season in UW football history, Willingham decided to let Baer go. In the three years at UW, the defense ranked 94, 95 and 98 in total defense, 89, 85 and 94 in scoring defense, and 106, 102 and 85 in passing defense.(1) On April 14, 2008, Baer became defensive coordinator at
San Jose State under
Dick Tomey. On December 11, 2012, Baer became interim head coach of San Jose State after
Mike MacIntyre resigned to become head coach at
Colorado. Baer coached the Spartans to a 29-20 victory over
Bowling Green University in the
2012 Military Bowl on December 27. MacIntyre announced on December 18 that he would like Baer to join him in Colorado as defensive coordinator. With five other former San Jose State assistants, Baer joined MacIntyre in Colorado on January 3, 2013. First year head coach
Tony Sanchez completed his staff at
UNLV when Baer joined on December 22, 2014 as his defensive coordinator and linebackers coach. Following the
2017 football season, Baer was relieved of his duties as defensive coordinator and linebackers coach at UNLV, allowing over 31 points per game and over 450 yards to opposing offenses. ==Head coaching record==