His decision has sparked speculation about who his successor could be.
We look at some of the likely candidates to be the next Conservative Party leader and prime minister.
The leading figure in the Vote Leave campaign and the bookies' favourite for the job, he has always been popular with the Eurosceptic Conservatives grassroots.
The former London mayor previously insisted he had less chance of taking the top job from his old Eton school mate than being "reincarnated as an olive".
Now it appears he is in pole position for the job.
The longest-serving home secretary (six years and counting), Theresa May has been a central figure of David Cameron's government.
Despite being a remain supporter, she was a fringe figure in the campaign, leaving her relatively unscathed from its failings.
She has been quietly courting the party's rank and file in readiness for Mr Cameron's departure and is placed by the bookies as second to Mr Johnson.
The Justice Secretary has seen his public profile increase over the past few weeks and he is generally regarded to have had a good campaign for Vote Leave.
Mr Gove, whose once close friendship with Mr Cameron has come under strain during the referendum campaign, is being given 5/1 odds of moving into Downing Street, despite him claiming he does not want the job.
At one point considered a favourite for the job, the chancellor's hopes have faded because of his close ties to Mr Cameron.
An upturn in economic fortunes under Mr Osborne's stewardship saw his popularity in the party increase, but backbenchers said his decision to back remain ensured any leadership bid was dead in the water.
She is still an outsider compared to Mr Johnson and Mrs May, but Tory leadership contests tend to throw up some surprises.
The other contenders
Work and Pensions Secretary Stephen Crabb is hugely popular in the Conservative parliamentary party and comes from the sort of ordinary background that chimes with many voters.
Scottish Conservative leader Ruth Davidson has done well during the campaign, but she would need to find a Westminster seat to get the top job.
Leave campaigner Priti Patel is another who features high in the betting, with odds as short as 8/1 on Friday.
The odds on the new leader
These were the odds provided by Ladbrokes on the new leader on Friday afternoon:
So how will the election process work?
Nominations for the new leader come from Conservative MPs.
If one nomination is received, they are declared the new leader. If two are received, both names are put to a ballot of party members across the UK.If three or more people are nominated, then a ballot of the 330 Conservative MPs is held "on the Tuesday immediately following the closing date for nominations" to whittle the pack down to two.
Once two front runners have been selected, the candidates then go head to head in a postal ballot of the wider party membership, which according to a House of Commons Library report stands at around 149,800 people.
This means they could be elected on the votes of just tens of thousands of people.