Brey guided the Fightin' Blue Hens to a 99–51 record over five years, leading the team to two America East Conference Championships and subsequently two trips to the NCAA Tournament.

In 2000, Brey succeeded Matt Doherty as head coach of the Notre Dame Fighting Irish men's basketball team.

Brey led the Irish to the NCAA tournament in his first three years as head coach (2001–2003), notching a Sweet Sixteen appearance in 2003.

On June 19, 2012, Brey signed a 10-year extension to remain the head coach of the Notre Dame Irish up until 2022.

He also passed Hall of Famer George Keogan for second place on Notre Dame's all-time wins list, trailing only Digger Phelps.

Notre Dame advanced to the Elite Eight for the second consecutive season, defeating Michigan, Stephen F. Austin, and Wisconsin as the 6 seed in the East region.

Notre Dame dominated its first two games against Virginia and Florida State and sparked another ACC tournament final appearance for the second time in three years.

[14] He would reunite with then-head coach Quin Snyder, who played his junior and senior seasons at Duke while he was an assistant under Mike Krzyzewski.