The senior diplomat had been expected to lead the UK's Brexit negotiations with the economic bloc but was recently in the eye of a storm following the leak of an internal memo in which he claimed leaving the EU could take up to a decade.
The UK Foreign Office confirmed the resignation today but declined to give any reasons behind the move at this stage.
Labour MP Hilary Benn, who chairs the UK Parliament's Brexit Select Committee, said the resignation had come at a "crucial" time. "It couldn't be a more difficult time to organise a handover," he said.
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Rogers, a veteran civil servant, was due to leave his post in November 2017 but is stepping down early.
Last month, the BBC revealed he had privately told ministers a UK-EU trade deal might take 10 years to finalise.
Prime Minister Theresa May has announced her intention to invoke Article 50 of the Lisbon Treaty to trigger official talks for Britain's exit from the EU by the end of March.
Rogers was expected to play a central role in those deliberations. However, now the government will need to put a replacement in place.
Leave EU, a pro-Brexit campaign group, tweeted: "Pessimist Rogers - who warned Brexit would take 10 years - is to leave his post as UK Ambassador to the EU. Good - time for some optimism!"