Andrew McCabe, 49, had been investigating Hillary Clinton and Trump's ties to Russia before the fallout.
The man who until recently was the FBI's deputy director, Andrew McCabe, has been fired from the agency by the US Attorney General Jeff Sessions.
The decision was taken "after an extensive and fair investigation" into McCabe, Sessions said, adding that he was fired for making an unauthorised disclosure to the media.
President Donald Trump delighted in the sacking on Twitter, calling it "a great day for working men and women of the FBI".
McCabe was deeply involved in the agency's investigations of Hillary Clinton and Russia's role in the U.S. presidential election, making him a frequent target of attack on Twitter by Trump.
The move came two days before his 50th birthday, when he was expected to retire with a pension - which could now be in doubt.
He had been on leave since January, when he stepped down amid deteriorating relations between the Trump administration and the FBI.
McCabe said he had been "singled out" in what he called the Trump team's "war" on the agency.
In an 848-word statement, he said: "For the last year and a half, my family and I have been the targets of an unrelenting assault on our reputation and my service to this country.
"Articles too numerous to count have leveled every sort of false, defamatory and degrading allegation against us. The President's tweets have amplified and exacerbated it all.
"He called for my firing. He called for me to be stripped of my pension after more than 20 years of service."