BBC Political Editor Laura Kuenssberg has tweeted to say that Mr Cummings will leave his Downing Street post by the end of 2020.
Mr Cummings told the BBC “rumours of me threatening to resign are invented,” after speculation this week.
But he went on to say that his position has not changed since a blog he posted in January in which he said he wanted to make himself “largely redundant” by the end of 2020.
A senior Downing Street source told the BBC that Mr Cummings would be “out of government” by Christmas.
The news follows a behind-the-scenes power struggle at No 10 this week in which Lee Cain, the director of communications and friend of Mr Cummings, stood down.
The pair worked together on the Leave campaign during the EU referendum.
Cabinet minister Grant Shapps said Mr Cummings "will be missed", but that he was not surprised the aide is departing, adding: "Advisers do come and go."
Conservative MPs urged No.10 to use his departure as an opportunity to restore the values of "respect, integrity and trust".
Labour told the government to focus on the coronavirus pandemic and not "self-indulgent spin doctors".
Meanwhile, the Treasury has settled an employment tribunal claim with a former aide who was fired by Mr Cummings. It is understood the government will be paying out a five-figure sum.
The settlement with Sonia Khan, who advised then-chancellor Sajid Javid until she was escorted out of Downing Street by police, means Mr Cummings no longer faces the prospect of giving evidence in the case next month.
Mr Shapps argued Mr Cummings, whose infamy was cemented by his trip to Durham during the first lockdown, is leaving because his big projects of coronavirus mass testing and Brexit being "on the near-term horizon now".
"He will be missed, but then again we're moving into a different phase," the Transport Secretary told Sky News, adding that "advisers do come and go".
Conservative MPs have urged Mr Johnson to use events to reshape the team inside Downing Street and reconnect with the parliamentary party, some of whom feel he has been "lost" to advisers over the past year.
Senior Tory backbencher Sir Bernard Jenkin told BBC Radio 4's Today programme: "It's an opportunity to reset how the government operates and to emphasise some values about what we want to project as a Conservative Party in Government."
He said it was time to restore "respect, integrity and trust", which he said have been "lacking in recent months" between No.10 and Tory MPs.
"I'm not surprised in a way that it is ending in the way it is,” he said.
"No prime minister can afford a single adviser to become a running story, dominating his government's communications and crowding out the proper messages the Government wants to convey. Nobody is indispensable."
Tory MPs openly aired their criticism after the infighting spilled into the open.
Conservative backbencher Sir Roger Gale said: "The government, and Downing Street particularly, should be concentrating all of its efforts on the pandemic and on the end game of Brexit."