A two-time First Team All-Conference selection, he was named Southwest Conference Player of the Year in 1960.  Harris was nicknamed "Thumper" for his hard hits, and the Arkansas coaches now honor the best defensive player with the Thumper Award. A true scholar-athlete, Harris was named First Team Academic All-America in 1959 and twice earned First Team Academic All-Conference honors.

Wayne Harris was honored with induction into the College Football Hall of Fame in 2004 after the National Football Foundation tabulated their votes. He was further honored in 1976 when the Canadian Football Hall of Fame inducted him for his play with the Calgary Stampeders.