In February 1995, Brady Hoke was hired as an assistant coach at Michigan under head coach Gary Moeller. He was the defensive ends coach in 1995 and 1996 and became the coach for the entire defensive line from 1997 to 2002.
In May 2002, Michigan head coach Lloyd Carr named Hoke as associate head coach, the only member of the staff with that distinction. At the time, Hoke told the press, "Every year you learn more and more what the head coach has to do. I'm very honored to represent this school. I grew up a big Michigan fan, and I think it's a place that's special in a lot of ways."
During Hoke's eight years at Michigan, the Wolverines compiled a 75–23 record, went to a bowl game every year and won the national championship in 1997. While at Michigan, Hoke was assigned to recruit in California. One of the players Hoke recruited to Michigan was Tom Brady. Hoke recalled: "Tom wasn't the greatest athlete, with those skinny legs, but there was something about him.