Nutt became the head coach of the University of Arkansas Razorbacks on December 10, 1997 succeeding head coach Danny Ford. On November 23, 2007 in Baton Rouge, Nutt’s Razorbacks beat the top-ranked football team in the nation. In a game that lasted into three overtime periods, Arkansas defeated the formidable and eventual national champion LSU Tigers, 50–48, returning the Golden Boot back to Arkansas. Nutt stayed on as the head coach from 1997-2007. When he resigned in November, he left the school with a 75-48 record, which is second on the school’s all-time win list, behind only Frank Broyles.

Houston Nutt is currently the head football coach at the University of Mississippi (Ole Miss), a position he has held since 2008.  Nutt’s wife Diana also graduated from Oklahoma State University. They have four children together: Houston III,  twins Hailey and Hanna, and Haven.