The senior diplomat had been expected to lead the UK's exit talks with the European Union (EU) but was recently in the eye of a storm following the leak of an internal memo in which he claimed leaving the union could take up to a decade.
The UK Foreign Office had confirmed his resignation yesterday but declined to give any reasons.
"We do not yet know what the government will set as negotiating objectives for the UK's relationship with the EU after exit," his note to his former colleagues in Britain's mission in Brussels reads.
"There is much we will not know until later this year about the political shape of the EU itself, and who the political protagonists in any negotiation with the UK will be," it added.
"I hope you will continue to challenge ill-founded arguments and muddled thinking and that you will never be afraid to speak the truth to those in power. I hope that you will support each other in those difficult moments where you have to deliver messages that are disagreeable to those who need to hear them," he said in the letter.
A spokesperson said: "Sir Ivan Rogers has resigned a few months early as UK permanent representative to the European Union. Sir Ivan has taken this decision now to enable a successor to be appointed before the UK invokes Article 50 by the end of March."
While the Brexit camp has welcomed this resignation, those against Brexit believe Rogers' exit marks a blow to the negotiations.
British Prime Minister May, who has said she plans to invoke Article 50 to trigger official Brexit talks by the end of March, is being pressured to appoint a pro-Brexit replacement for Rogers.
Rogers occupied the post of theUnited Kingdom Permanent Representation to the European Union (UKRep), which represents the UK in negotiations that take place in the EU.
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