Cyclones coach Paul Rhoads announced Friday that Barnett and linebacker C.J. Morgan will be transferring.
Barnett led the Cyclones to the biggest win in school history in 2011, throwing for 376 yards in a win over then-No. 2 Oklahoma State. But Barnett lost his starting job to senior Steele Jantz twice in 2012, while freshman Sam Richardson took over as the starter for the final two games of the season.
Barnett threw for 1,825 yards and 12 TDs at Iowa State.
Rhoads says Morgan has some health issues with his family and is looking to play closer to home.