Some of the political fallout from Copenhagen has been directed at the Dutch former civil servant, accused from the sidelines of having over-stoked expectations and promoted issues favouring developing countries.
"There are people who say I overstepped the boundaries of my job description," de Boer was quoted by the AFP news agency as saying.
"I actually don't have a job description. But if I had one, I am sure I would have overstepped the boundaries and I did that consciously, because I think that this is an issue that needs to be elevated to the top of the political agenda."
The Copenhagen summit, held in Denmark last December, ended with only voluntary pledges to cut emissions and no clear details on how those goals will be achieved.
But its supporters point out it that it did bring rich and poor nations together and agree $30bn for poor countries by 2012 to help them tackle climate change.
In the run-up to Copenhagen, de Boer had said anything less than agreement on emissions caps for individual developed nations would count as failure.
But he also warned African nations and small island states that their calls for deep cuts by the developed world represented "too heavy a lift".
De Boer's departure takes effect five months before 193 nations reconvene in Cancun, Mexico, for another attempt to reach a worldwide legal agreement on controlling greenhouse gas emissions
Agus Purnomo, Indonesia's special presidential assistant on climate change, said the news "comes at the worst time in the climate change negotiations".
"His decision will ultimately add to the difficulties we already have in reaching a successful outcome in Mexico."
Others felt the talks would move ahead despite de Boer's departure.
"A change of leadership ... provides a fresh opportunity to re-energise international negotiations ahead of the UN climate summit in Mexico,'' Steve Howard, from The Climate Group a UK-based organisation, said.
De Boer, who once left a UN meeting in Bali in 2007 in tears after a Chinese delegate criticised the secretariat for starting a key meeting before all delegates were present, leaves no obvious successor.
Ban Ki-moon, the UN secretary-general, will make the final a decision on a replacement, a UN spokesman said.