The former Canaries player took charge in January and was unable to guide the club to safety at the wrong end of the Championship.
Gunn told the club's official website: "With League One football it was important that the board decided what the management team was going to be.
"I'm absolutely delighted that they have chosen myself, Ian Butterworth and Ian Crook to take the club forward.
"We are all looking forward to the challenges of League One and we are all bitterly disappointed with what happened last season. Now is the time to look forward and prepare for what is a very important season.