Gunston was called into the stand-in role after Ian Robson quit mid-season, following the supplements scandal that engulfed the Bombers.
He confirmed on Monday he would not be seeking the position on a full-time basis, advising the Essendon board that he would be vacating the role.
Gunston was a key player in Essendon accepting its penalty from the AFL for bringing the game into disrepute in August, when the League handed down its biggest ever sanction to a club.
He also helped oversee the appointment last week of Mark Thompson as senior coach for next season while James Hird serves his suspension.
Bombers chairman Paul Little said the "requirements of the interim role are largely fulfilled".
"Ray will finish up with the club later this year after helping in the process of appointing the permanent CEO," Little said in a club statement.
"Although obviously joining us at a very challenging time earlier this year in the middle of the investigation, Ray has assisted to lead the club through this and to provide the sound base for the future success of the club in the short time he has been in the role."
Twitter: @AFL_CalTwomey
