Mr. Johnson has spoken to Tory 1922 Committee chairman Sir Graham Brady and agreed to stand down, with a new Tory leader set to be in place by the party conference in October, a No 10 source said.
It comes after his newly appointed Education Secretary Michelle Donelan resigned after 36 hours in the post, Chancellor Nadhim Zahawi told the prime minister to “go now” and Defence Secretary Ben Wallace withdrew his support.
It follows intense pressure from party colleagues, with dozens of resignations within government from cabinet level down.
Rishi Sunak resigned as chancellor and Sajid Javid quit as health secretary on Tuesday night.
That prompted a flood of resignations from government as Tory MPs said they could no longer support a leader who has lied over the appointment of deputy chief whip Chris Pincher, plunging the PM into further crisis.
At PMQs on Wednesday, he dismissed calls to quit.
The resignations began after Downing Street insisted the PM did not know about 2019 allegations of inappropriate behaviour against disgraced MP Mr Pincher before appointing him as deputy chief whip in February.
On Wednesday, No 10 admitted Mr Johnson in fact had known about the claims – and subsequent investigation.
Cabinet minister Michael Ellis said the PM “did not immediately recall” he had been told in 2019, but had been reminded.