Speaking at the Convention of the North this afternoon Mr Johnson said new powers would be given to northern areas to control their transport links.
Mr Johnson said he was giving power back to "where [the railways] were born" and handing over control of service patterns, rolling stock and stations to combined authority areas, county councils or community rail partnerships.
He said: "Today, coming from London, on the train, It took me just over an hour and a half to get to Doncaster. But if, for example, you are travelling from Liverpool to Rotherham - less than half the distance - you might have had to leave an hour earlier than me and change as many as three times.
"Your journey may have been on two and three carriage trains, some of them built in the early 1980s with a body designed for a bus and maybe bus seats, too. I love buses, but not when they're supposed to be trains."
Mr Johnson said Merseyrail and Manchester's transport system were examples of where things worked well. But he said the common factor there was they were run locally.
Mr Johnson said: "All too often northern England has to put up with old diesel trains running once or twice an hour from stations where the only form of welcome on the platform is a bus shelter.
"Each of those well-running services is run on behalf of locally elected politicians, and they always care more about their trains than someone in Whitehall. London was just the same before 2000 when London transport was run by central government. The tube was frankly shabby and neglected. But when my predecessor and I ran it services improved there."
But he warned the advantages came with having to take responsibility if things went wrong too.
He said: "Now, we will be generous on capital spending but we won't be able to afford everything everyone wants. So choices will have to be made. And if you people want more than they can afford, they will have to raise the money themselves.
"And of course the North's railways must still be part of the national network. This will be a partnership between the railways and the leaders of the North. And I think it's a formula that can work and it will deliver better services for the people of this country."
Mr Johnson was also quizzed on devolution after he last week said he was "mad keen" in principle on a One Yorkshire deal.
Today he said he wanted to "open up negotiations" for deals in Leeds and West Yorkshire, but stopped short of saying this could lead to a wider arrangement.
He said: "We will get on as fast as possible [with Leeds and West Yorkshire] and whether it leads to a deal for the whole of Yorkshire or not, that is very much a matter of consultation and decision led by local people.
"I know that there are different views. And I've been I've been speedily acquainted of those different views and the strength of feeling which is held on either side. There are clearly different areas that could elect a mayor and I think that there needs to be further work done on that precise geographical division."
Judith Blake, Leader of Leeds City Council and West Yorkshire Combined Authority Transport Lead, said: “We look forward to the Williams Review clarifying how the Prime Minister’s commitment to local control of rail services will work in practice to the benefit of passengers, communities and business in our region and without introducing further fragmentation.
“We would welcome the opportunity to have a greater say in how local rail services are delivered but this significant responsibility must come with the associated powers and funding to address historic under investment in the North’s rail network which as at the root of its current failings.”