Houston Nutt, Jr. was born in Arkansas. He is the son of the late Houston Dale Nutt, Sr., and Emogene Nutt and is the oldest of four children. Wife Diana, like Houston, graduated from Oklahoma State University. They have four children together: Houston III, twins Hailey and Hanna, and Haven. Nutt initially played collegiately at Arkansas and started four games as a true freshman. After a coaching change Nutt transferred to Oklahoma State and played two years before graduating in 1981 with a degree in Physical Education.

After being a graduate assistant at Oklahoma State and Arkansas he went on to coach receivers and quarterbacks at Oklahoma State in 1984 and became offensive coordinator in 1989 and coached Heisman Trophy winner Barry Sanders as well as future Buffalo Bills legend Thurman Thomas. Nutt returned to Arkansas in 1990 as an assistant and got his first head coaching job at Murray State in 1993. He went 11-1 in 1995 at Murray State and won the Ohio Valley Coach of the Year as well at the Eddie Robinson National Division 1-AA Coach of the Year Award. He moved on to become the head coach of Boise State for the 1997 season before becoming the head coach at Arkansas from 1998-2007.

While at Arkansas Nutt won the SEC West twice and was named the SEC Coach of the Year in 2001 and 2006. Nutt was also named The Football News Division 1-A Coach of the Year in 1998. In his final game at Arkansas the Razorbacks beat #1 ranked and eventual national champion LSU 50-48.

Nutt was hired at Ole Miss shortly after his resignation at Arkansas. In his first season in Oxford he was named the SEC Coach of the Year and the Rebels defeated the eventual National Champions Florida Gators in Gainesville. He led the Rebels to the Cotton Bowl in his first two seasons in Oxford.