Corcoran was suspended by the AFL in August for his role in the Bombers' controversial supplements program.
Coach James Hird was suspended for a year and senior assistant Mark Thompson was fined $30,000.
The club was also hit with a $2 million fine and draft penalties and was banned from participating in the 2013 finals series for bringing the sport into disrepute.
"I took the general manager of football role to implement a succession plan and knowing in time I would help the club find the right person to succeed me," said Corcoran, who has told the club he is prepared to help in the transition period while they searches for his successor.
"Over the last couple of months I've had the opportunity to step away from everything, travel and reflect on a difficult year and I have decided that now is the right time for me to consider the next phase of my life.
"I've enjoyed my time working at Essendon with a number of highly professional and quality people.
"I wish the club every success in the future."
In other news, the Bombers have been unable to find a suitable replacement for Ian Robson, who stood down as chief executive in May.
The position will remain vacant until further notice, with new chief operating officer Xavier Campbell taking over the senior executive role under the new structure.
Essendon chairman Paul Little and finance director Paul Brasher have also had their roles expanded.
Interim CEO Ray Gunston formally ends his time at the club on December 31.
"The board decided the short-listed candidates for the CEO role didn't provide all of the qualities we believed (were) required to adequately fill this demanding role," said Little.
"It was determined the club would promote from within and create a new chief operating officer position to manage the key areas of the business."
Robson became the first casualty of the supplements saga when he stood down in May, admitting he was accountable for what happened on his watch.
"We now know that a lot happened at this club in 2012 that just should not have happened," Robson said when announcing his resignation.
"We let down our players and their families; how seriously we let them down is still a matter of investigation.
"There is no excuse in not knowing, and as CEO, I am accountable and I accept that accountability."
Robson is now the CEO of A-League club Melbourne Victory.