In an official confirmation of Duncan's resignation after weeks of speculation, Channel 4 chairman Luke Johnson, said: "When the time comes he will depart with our best wishes for his future success.
"In the meantime, we will immediately get on with the process of appointing his successor. We will move swiftly to appoint headhunters with a view to appointing a replacement in due course.
"I have asked our finance director, Anne Bulford, to lead the group on an interim basis in the event that Andy leaves before this successor is in place."
This morning Duncan informed the Channel 4 board of his decision to step down from his post before the end of the year.
He admitted discussions over his future had started with the publication of the Digital Britain report in June, arguing that this had seen Channel 4 secure its future as "the main source of public service competition to the BBC".
"The publication of the Digital Britain report was also a natural moment for me to take stock and since then I have been in discussion with Luke and other board members about the future," Duncan said.
"Channel 4 is facing a further period of change, with a fresh regulatory cycle looming and with the cancellation of Big Brother signalling the most significant creative renewal in our history. We have mutually agreed that this feels like the appropriate moment for me to hand on the baton to someone else and to move on to a fresh challenge after more than five years at the helm."
"My intention in announcing my decision in advance is to ensure a period of stable leadership, which will allow the board to proceed with recruiting my successor in parallel with Ofcom's appointment of a new chairman. I hope that clarifying my intentions will allow everyone at Channel 4 to get on with the job at hand without the distracting speculation of recent weeks.
"In my remaining months I intend to see through important further steps towards securing the best possible future for this organisation, including the update of our remit and the completion of a number of exciting commercial partnerships currently under discussion."