After completing college, Hughes became an assistant coach for both baseball and football at
Hamilton College. He stayed there for one academic year before moving to
Northeastern in the same dual capacity. After five years, he decided to focus on baseball and landed his first head coaching job at
Trinity University in Texas. Taking just two seasons to improve the Tigers to a conference championship, Hughes was hired by
Boston College after the 1998 season. His success with the Eagles was also immediate, improving Boston College's record by nine wins in his first year. Hughes picked up a variety of Coach of the Year awards in his second season, including awards from the
Big East Conference and regional selectors of the
American Baseball Coaches Association. He would earn more such honors in 2002 and 2005. He also led the Eagles to the
Big East Conference baseball tournament five times in seven years. Boston College had only appeared in the tournament once prior to his arrival. Hughes earned a three-year contract extension after the 2009 season. He was hired by the
Oklahoma Sooners in 2014. He was let go by the Sooners in June 2017. On July 31, 2017, Hughes was named volunteer assistant at Georgia. On June 8, 2018, Hughes was named the head coach of the
Kansas State Wildcats baseball team. ==Head coaching record==