Mr Johnson also used a keynote address in Manchester to pledge funding for a high speed rail link between the city and Leeds, as well as a boost for broadband connectivity and extra resources for crime-fighting.
And he promised to give greater powers to council leader and communities and "level up the powers offered to mayors" to help boost cities, towns, coastal communities and rural areas.
The PM, who wore a badge bearing the phrase "Northern Powerhouse" during the speech, said: "We are going now to have a £3.6 billion Towns' Fund supporting an initial 100 towns, so that they will get the improved transport and the improved broadband connectivity that they need."
The £1.6 billion Stronger Towns Fund for England was launched in March this year by previous Communities Secretary James Brokenshire.
Mr Johnson said: "This might come as a surprise to some, but not everyone wants to live in one of our country’s great cities.
"Too many places - towns and coastal communities - that don’t feel they are getting benefits from the grown we are seeing elsewhere in the UK economy.
"Now I reject the ridiculous idea that everybody's ambition is to get on their bikes and move to the city.
" Our post-industrial towns have a proud, great heritage - but an even greater future. Their best years lie ahead of them. So we are going to put proper money into the places that need it."
Thirsk and Malton MP Kevin Hollinrake described the towns fund as "really fabulous news". He told The Yorkshire Post: "City regions are hugely important but we must not leave behind our towns, villages, rural areas and coastal communities.
"It's very good news that the new PM recognises this and I'm sure that it's, in part at least, a result of the influence of Rishi Sunak, Nigel Adams and Jake Berry."
In a reshuffle by Mr Johnson, Jake Berry will now be attending Cabinet as Northern Powerhouse Minister, while Rishi Sunak and Nigel Adams have both been handed ministerial roles.
Meanwhile Wigan MP Lisa Nandy, part of the Centre for Towns think-tank, wrote on Twitter: "Our great towns used to power the world through the mills, mines and factories that were closed by the last Tory Government, so forgive me if I’m sceptical of this PM, gearing up for a General Election, who has never bothered to ask us what we want or need."
Will Jennings of the Centre for Towns think-tank added: "Of course, it is one thing to talk, it is another to deliver. Towns are not all alike and face a wide range of policy challenges that won't simply be solved by splashing the cash.
"Those challenges are a product of fundamental economic processes relating to agglomeration... until those are addressed, the same dynamics of decline will persist in peripheral areas."
Last year, The Yorkshire Post revealed that the region faces a demographic time-bomb that threatens to “rip the heart out” of many towns and villages and distance them further from the region’s thriving cities.
Population projections show that the combination of an ageing population and the drift of the working age population to major urban centres seen in recent decades will continue to dramatically re-shape Yorkshire in the coming years.
Analysis by the Centre for Towns reveals that the number of over-65s in the region is set to increase by a massive 42 per cent by 2038, while the overall population rises by just six per cent.
Towns and villages are forecast to become much older in the next two decades, increasing the dependency of residents on the working age population, while cities and bigger towns are expected to age at a much slower rate.
In a clear pitch to traditional Labour voters yesterday, Mr Johnson insisted that politicians had failed people in the North.
He said: "The centre of Manchester, like the centre of London, is a wonder of the world. A few miles away from here, the story is very different.
"The story has been for young people growing up there of hopelessness, or the hope that one day they will get out and never come back.
"The crucial point is it certainly isn't really the fault of the places, and certainly isn't the fault of the people growing up there. They haven't failed. It's we, us, the politicians, our politics has failed them."
Mr Johnson set out the four "ingredients" for the success of the UK as livability, connectivity, culture, and power and responsibility.
He said this means areas having great public services, enough affordable homes, safe streets, fast broadband, and more responsibility and accountability for local areas.
He added: "I want to set out what I think are the ingredients for the success of the UK, the places we call home whether it's our cities or our towns, our coastal communities or rural areas.
"We are going to give greater powers to council leaders and communities.
"We are going to level up the powers offered to mayors so more people can benefit from the kind of local structures seen in London and here in Manchester."
Mr Johnson used the speech to state he is committed to "rebalance power, growth and productivity across the UK".
The PM pledged to "improve the unglamorous local services which people use every day", such as buses, saying it is about "services within cities, not just services between cities".