The senior diplomat had been expected to lead the UK's Brexit negotiations with the 28-member EU but was 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.
Rogers occupied the post of the United Kingdom Permanent Representation to the European Union (UKRep), which represents the UK in negotiations that take place in the EU.
UKRep is one of the busiest posts, with a team sourced from over 20 UK government departments working to ensure that UK policies are explained to other EU member states, the European Commission and members of the European Parliament.
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Last month, the BBC revealed he had privately told ministers a UK-EU trade deal might take 10 years to finalise.
The leak of the private memo is believed to have caused him a lot of embarrassment and strained relations with Downing Street.
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.
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A Foreign Office 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. We are grateful for his work and commitment over the last three years".