Mr McCabe, 49, who was already expected to step down in early 2018 upon becoming eligible for his pension, instead chose to step down now and is on leave ahead of his official retirement date, CBS News reports.
As reported earlier this month by the Washington Post, Trump lashed out after hearing that a political action committee aligned with Hillary Clinton provided campaign funds to McCabe's wife for a failed 2015 Virginia state Senate bid.
Trump once asked McCabe how he voted in the 2016 presidential election, The Washington Post reported.
White House press secretary Sarah Sanders said Trump was not part of McCabe's choice to step down and that the White House had not been part of the decision.
McCabe's decision comes amid a flurry of reports on the Trump administration's displeasure with the FBI and the US Justice Department amid the ongoing Trump-Russia investigation.
Mr Trump's firing of Mr Comey in May 2017 as the FBI was investigating potential collusion between Mr Trump's 2016 presidential campaign and Russian Federation led to the Justice Department's naming of Special Counsel Robert Mueller to take over the probe. After all, without the October 28 letter, which turned out to be nothing but more meaningless email noise, there's a good chance Hillary Clinton would be in the White House today. Once Trump appointed Christopher Wray, McCabe went back to the deputy director position. It's worth remembering that McCabe is far from the only Justice Department official Trump has tangled with since becoming president.
"I don't think I did", Trump told reporters about asking who McCabe voted for.
McCabe made his intentions known to colleagues Monday, a USA official said.
McCabe has been targeted by GOP lawmakers, who criticize the Federal Bureau of Investigation over its handling of the probe into Hillary Clinton's use of a private email server, a probe that included McCabe.
A few hours later, McCabe told him the bureau couldn't start the practice of commenting on newspaper stories or it would never end.
A handful of Republican-led congressional committees have also launched inquiries into whether the FBI botched the Clinton investigation and showed bias in her favour.