The Prime Minister said he was concerned about the cost of the line, which is set to pass through 45 miles of Staffordshire countryside on its way from London to the north.
The figure puts the bill for HS2 at almost double the £56bn figure that Theresa May's government claimed it would cost.
Speaking on a visit to the West Midlands, Mr Johnson said the cost would "probably be north of £100 billion", and that it was "only responsible" for a new government to review the project.
The claim came ahead of a keynote speech on Saturday where the Prime Minister made funding pledges for variety of schemes, including for a new rail link between Manchester and Leeds, as he sought to shift the spotlight from Brexit to his domestic agenda.
The PM gave his backing to the trans-Pennine transport link between Manchester and Leeds which is intended to help “turbo charge” regional growth.
Mr Johnson said: “I want to be the PM who does with Northern Powerhouse Rail what we did with Crossrail in London.
“And today I am going to deliver on my commitment to that vision with a pledge to fund the Leeds to Manchester route.
"It will be up to local people and us to come to an agreement on the exact proposal they want – but I have tasked officials to accelerate their work on these plans so that we are ready to do a deal in the autumn.”
Downing Street said that detailed plans regarding the proposed route will be published in the autumn, following the review into HS2.
'Fanatical about infrastructure'
There has been intense speculation that Mr Johnson could ditch HS2 altogether.
He has appointed engineering expert Doug Douglas Oakervee to review the project, who he said will be tasked with looking at "the profile of the spend".
"I want him to establish where there's waste, if there's waste and whether it can be re-profiled in any way," Mr Johnson said in Birmingham on Friday.
"But I want to stress to everybody that there is noone more fanatical about major infrastructure projects than me. I do believe in their potential. I was the Mayor who delivered Crossrail, for London's biggest engineering project in Europe.
"I want to hesitate for a long time before scrapping any major infrastructure project, but I think it is only responsible as an incoming government, with all the controversy surrounding the spend on HS2 – which will probably be north of £100 billion – it is only responsible to have a review over a short period, without in any way interrupting the timetable."
Labour’s shadow transport secretary Andy McDonald was dismissive of the Manchester-Leeds rail pledge, stating: “This project has been announced time and time again by the Conservatives.
“With Boris Johnson’s staggering failure to build a bridge across the Thames and an estuary airport I’m not confident he’ll be able to deliver better train services between Leeds and Manchester.”
Mr Johnson has appointed HS2 opponent Andrew Gilligan as a transport advisor, a move from which he said "no conclusions shall be drawn".
Mr Gilligan has been a critic of the line since its inception, describing it as a “disastrous scheme” that cannot possibly be built to budget, and arguing for a slower and cheaper line to be built instead.
The project's cost has come under close scrutiny this year, with a Lords' report questioning whether it could be built to budget and demanding a new inquiry into its economic case.
And Allan Cook, the new chairman of HS2 Ltd, has reportedly written to the Department for Transport (DfT) warning that the scheme could cost £85bn – almost treble its initial budget from 2010.
West Midlands Mayor Andy Street has insisted HS2 must be built to help boost the region's economy.