But White House officials have insisted that Mr Trump was not involved in the decision.
Citing “a source familiar with the matter”, Reuters news agency said Mr McCabe was leaving his post immediately, despite the fact he had been due to stand down in March.
Mr McCabe, who served as acting Federal Bureau of Investigation chief for more than two months last year after Mr Trump fired agency director James Comey, will remain on leave with the top US domestic law enforcement agency until his retirement date, the source said, speaking on condition of anonymity.
No official announcement has yet been made about the situation, and an FBI spokeswoman declined to comment when asked.
Asked by reporters about McCabe’s departure, White House spokeswoman Sarah Sanders said: “I can tell you the president wasn’t part of this decision-making process.”
She said Mr Trump continued to have “full confidence” in FBI Director Christopher Wray, whom the president appointed to replace Mr Comey.
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 Russia led to the Justice Department’s naming of Special Counsel Robert Mueller to take over the probe.
The President later said he dismissed Mr Comey over “this Russia thing,” and the firing has become central to questions about whether Mr Trump has sought to obstruct justice by impeding the Russian probe.
Mr Trump last week denied a story in the Washington Post suggesting he had asked Mr McCabe, shortly after he became acting FBI director, who he had voted for in the 2016 presidential election, leaving Mr McCabe concerned about civil servants being quizzed about their political views. The Post reported that McCabe told Trump he did not vote in the election.
The US President and some other Republicans have been stepping up criticisms of the FBI in a move Democrats claim is part of a broader effort to undermine Mr Mueller’s investigation.
Republicans have criticised Mr McCabe in connection with the FBI’s investigation into Mrs Clinton’s use of a private email server while she served as US secretary of state. No charges were brought against her.
Republicans have also noted that Mr McCabe’s wife previously ran as a Democrat for a seat in Virginia’s state Senate and received donation funds from then-Virginia Governor Terry McAuliffe, a close ally of Hillary and Bill Clinton, the former president.
The FBI has previously said Mr McCabe was not involved in the Clinton investigation until he was promoted to deputy director in January 2016. By that time, his wife’s campaign was over and his involvement was not seen as a conflict.
Mr Trump, meanwhile, has repeatedly taken to Twitter to blast Mr McCabe, asking in December how he could be in charge of the Clinton probe when his wife got donations from “Clinton Puppets.”
Also on Twitter, during the period in which Mr McCabe was acting FBI chief, Mr Trump asked why Attorney General Jeff Sessions had not replaced him, and said in December McCabe was “racing the clock to retire with full benefits” and that the FBI’s reputation was in “tatters.”
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.
Democrats have said those inquires are aimed at undermining and distracting from Mueller’s investigation.
The Justice Department’s inspector general is conducting his own review into the FBI’s handling of the Clinton investigation, with Mr McCabe’s role is among those under scrutiny.