Martin joined the college ranks as an assistant coach/recruiting coordinator at Northeastern University from 2000 to 2004. He moved to the University of Cincinnati, serving one season each under Bob Huggins and Andy Kennedy. Martin followed Huggins to Kansas State, joining his staff on April 5, 2006. In 2007, almost a year to the day after his arrival in Manhattan, Frank Martin was made Head Coach of the Wildcats.

Martin led the 2007–2008 Wildcats to their first berth in the NCAA Tournament since 1996. He was awarded the Big 12 Conference Coach of the Year and later that month, he led the Wildcats to the Elite Eight, their deepest run in the tournament since 1988.

In 2012, Frank Martin accepted the head coach position at South Carolina.