The surprise move comes days after the airport (BER) CEO presented his progress report to a supervisory board for the still-under-construction airport on Friday where he said the airport requires a second terminal to handle anticipated passenger numbers.
Mehdorn said he would stay on until June 30th 2015 at the latest, two years the before earliest projected opening date for the airport in summer 2017.
The CEO said his resigned because of the level of supervision the airport was under. Since taking over the project in March 2013, he has not been shy about his grievance with the supervision, publicly calling it "the Inquisition" and accusing it of spreading the "culture of mistrust around BER".
"I personally regret my resignation very much because it corresponds with neither my sense of duty, nor with my personal ambitions," Mehdorn said in a statement.
His contract was to run until February 2016.
As recently as Friday, members of the supervisory board had supported Mehdorn in his position.
"Mehdorn is our chairman and has our trust," said supervisory board member Rainer Bomba on Friday.
Mehdorn is another nationally known figure dragged down by the airport. On Thursday last week, long-time Berlin mayor Klaus Wowereit resigned after the endless delays to the project stoked calls for him to go.
BER was originally scheduled to open in 2010, but has seen a string of delays in its opening dates since. The budget has ballooned from the original €2.83 billion to €5.4 billion and counting.
Additional costs to get the airport departure-ready are estimated between €2.19 billion and €3.2 billion.
Mehdorn was in charge of national rail carrier Deutsche Bahn, overseeing its restructuring. Prior to taking the BER job, he helmed Germany's second biggest airline, Air Berlin.
On Monday, new Berlin Mayor Michael Müller also told news radio programme that the supervisory board had ended its contract with a management consultant company. It was no longer willing to pay the bills.
BER was originally planned to replace the smaller, older Schönefeld and Tegel Airports in the Berlin area. The Berliner Zeitung reported on Sunday that €20 million is being invested into Tegel to keep it operating, as it was supposed to be shuttered in 2011.
"We are taking care of Tegel," said a speaker for the Tegel airport authority.
Mehdorn took over from disgraced CEO Rainer Schwarz, who successfully sued the BER airport authority for unlawful dismissal, winning €1 million in damages. On Monday, Berlin state courts announced that an appeal has been filed.