McCabe is stopping work immediately but will remain on the FBI payroll until March to obtain retirement benefits, the source confirmed.
McCabe, 49, was expected to leave sometime early this year when he became fully eligible for a pension, after two decades in the bureau.
The New York Times reported that McCabe had hoped to stay active in his position up to his retirement, but was pressured to leave earlier by FBI Director Christopher Wray.
Wray, who was appointed by Trump in August, had not intended to include McCabe on his revamped management team, according to the report. McCabe was a career FBI official, not a political appointee.
The FBI had no official comment. White House spokeswoman Sarah Sanders said Trump had no role in the move.
"The president wasn't part of this decision-making process," Sanders said.
The early departure comes after McCabe endured months of tough criticism from Republicans for his loyalty to fired FBI director James Comey and alleged bias against Trump.
McCabe and Comey had key roles in the FBI's probe of Trump's rival Hillary Clinton during the 2016 election, which ultimately cleared the Democrat of criminal wrongdoing in her misuse of a personal email server while she was secretary of state.
The president has repeatedly assailed that decision as wrong, and recently released text messages between two investigators involved in the Clinton probe that showed them strongly opposed to Trump.
An FBI inspector general is currently investigating the handling of the Clinton case.
McCabe and Comey were also involved in the initial stages of an ongoing investigation into whether the Trump campaign colluded with Russians during the election, which Trump calls "fake news."
Angered by that investigation, Trump fired Comey on May 9.
McCabe became acting FBI director and days later, in testimony to Congress, he rebutted Trump's claim that Comey had left the bureau "in turmoil" and had lost the confidence of the FBI staff.
Sharp attack from Trump
Accusations of bias also arose from McCabe's wife having run as a Democrat for local Virginia political office as a Democrat in 2015, receiving financial support from the party.
In July 2017. Trump questioned why Attorney General Jeff Sessions did not dismiss him.
"Why didn't A.G. Sessions replace Acting FBI Director Andrew McCabe, a Comey friend who was in charge of Clinton investigation but got big dollars ($700,000) for his wife's political run from Hillary Clinton and her representatives," he wrote on Twitter.
Trump named Wray the new FBI director in August, and kept up the pressure on McCabe. He tweeted again in December about McCabe's wife, and his role in the Clinton probe. He added a hint that McCabe was soon to depart, before it was publicly known.
"FBI Deputy Director Andrew McCabe is racing the clock to retire with full benefits. 90 days to go?!!!" Trump wrote.
Republican legislator Matt Gaetz called the move "a step forward" for the FBI.
"The past several weeks and months have seen worrisome evidence of bias and wrongdoing at the FBI come to light," said, referring to the investigators' anti-Trump text messages.
But McCabe retained strong support from within the Justice community, and Democrats have called Trump's pressure a part of a broader campaign to tarnish the bureau and weaken the Mueller collusion investigation.
Former attorney general Eric Holder lauded McCabe.
"FBI Deputy Director Andrew McCabe is, and has been, a dedicated public servant who has served this country well," Holder said.
"Bogus attacks on the FBI and DOJ to distract attention from a legitimate criminal inquiry does long-term, unnecessary damage to these foundations of our government."
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)