Sir Ivan was recently attacked by Brexit campaigners for "gloomy pessimism" after he reportedly warned Theresa May it could take ten years to negotiate the UK's exit from the EU.
Leave dot European Union labeled him "pessimistic".
Charles Grant, director for the Centre For European Reform and EU expert, tweeted saying Rogers' departure damages the United Kingdom government's hopes of negotiating a favourable Brexit deal with the EU, saying the seasoned diplomat is "one of the very few people at top of Brit govt who understand [the] EU".
"Sir Ivan Rogers has resigned a few months early as United Kingdom permanent representative", said a spokesperson.
But a gleeful Nigel Farage, suggested "a lot more" British diplomats should follow Sir Ivan Rogers and resign.
Sir Ivan Rogers has led the embassy since late 2013 - including guiding David Cameron's lengthy attempts at renegotiating United Kingdom membership a year ago, ahead of the fateful June 2016 referendum.
The former Ukip leader said: "The world has changed". His four-year term was expected to finish in November 2017. "The political establishment in this country and the diplomatic service just doesn't accept the vote", he said.
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According to the embassy, Sir Ivan will leave over the next few weeks, and had been due to leave in October.
Highlighting the timescale set by the PM to trigger the formal Article 50 process for leaving the EU, Mr Been said finding a replacement should be an "urgent priority" for the Government.
In his note to colleagues, Sir Ivan said: "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".
The research stated that the Britain would be over US$549 million a week better off through a mixture of taking back control of the money we give to the European Union each year, lower regulatory burdens on British businesses and through striking trade deals with growing parts of the world's economy.
"Our negotiation as a whole will go nowhere if ministers are going to delude themselves about the enormous difficulty and challenges Britain faces in implementing the referendum decision", he told The Guardian.
"Sir Ivan has taken this decision now to enable a successor to be appointed before the United Kingdom invokes Article 50 by the end of March".
"We are grateful for his work and commitment over the last three years", they added.