After growing up in Brockton, Massachusetts, Hughes attended Boston College High School, lettering in both baseball and football for the Eagles.

After five years, he decided to focus on baseball and landed his first head coaching job at Trinity University in Texas.

[1] Hughes was hired as head coach at Virginia Tech beginning in the 2007 season, replacing Hall of Famer Chuck Hartman, who had led the Hokies for the previous 28 years.

Hughes has rebuilt the Hokies into a power, bringing the team back into the national rankings and to the Atlantic Coast Conference baseball tournament on a regular basis.

On June 8, 2018, Hughes was named the head coach of the Kansas State Wildcats baseball team.