Electrification of key northern rail lines will now go ahead, the Government has announced just months after shelving the plans.
Transport Secretary Patrick McLoughlin said the overhaul of Midland Mainline and the TransPennine routes will restart following the so-called pause that was ordered in June.
The Government was accused of deceiving the public over its intentions for the rail network when the scheme was put on hold just weeks after the general election.
Its decision to restart the work comes just days before the Conservatives head to Manchester for the party's autumn conference.
Mr McLoughlin said: "As a one nation Government we are making sure every part of Britain benefits from a growing economy.
"Connecting up the great cities of the North is at the heart of our plan to build a Northern Powerhouse. This Government will see the job through and build a better, faster and more reliable railway for passengers in the North and Midlands."
Mr McLoughlin previously blamedNetwork Rail for the pause and told MPs none of the executive directors would get a bonus for the past year.
But the company insisted the three-month delay had allowed it to "develop a better plan for passengers".
Labour accused the Government of incompetence and claimed the delays had led to construction job losses.
Plans will now be drawn up for electrification of the TransPennine line between Stalybridge and Leeds and on to York and Selby.
It is expected to improve journey times and boost capacity between Manchester, Leeds and York.
The work is due to be completed by 2022 and will mean the whole route from Liverpool to Newcastle will be fully electrified, according to the Department for Transport.
Plans to upgrade the Midland Mainline include electrification of the line north of Bedford to Kettering and Corby by 2019 and the line north of Kettering to Leicester, Derby, Nottingham and Sheffield by 2023.
Shadow transport secretary Lilian Greenwood said ministers have been forced to change course after an "outcry" from passengers.
She added: "It's disappointing that these projects will be delivered years late, holding back the economies of the Midlands and the North while schemes in other regions go ahead as planned.
"We warned ministers for months that these projects were at risk, but they cynically waited until after the election to withdraw support.
"Their incompetence has led to a damaging hiatus, which has seen construction job losses and resources shifted to other projects; it is going to take longer and cost more to electrify these lines. Passengers will not tolerate any further delays to these vital projects."
Network Rail chairman Sir Peter Hendy said: "The temporary pause in the programme has given us the space to develop a better plan for passengers.
"People can expect more services and faster journeys. We face some difficult challenges, and there is more work still to do, but the Secretary of State's decision means we can now move forward with our plans to electrify TransPennine and Midland Mainline."
A spokesman for the Rail Delivery Group, which represents Network Rail and train operators, said: "The railway is crucial to Britain's prosperity, connecting people with jobs, friends and family so it is important to have continued and sustained investment in it.
"With ever more people being attracted to travel by train, it is good news that work to bring faster, more reliable and greener journeys to passengers in the North and on the Midland Mainline is to be restarted."
Ed Cox, director of the IPPR North think-tank, said the delays had been a "setback for the credibility" of the Government's so-called Northern Powerhouse project to boost the economy of the north of the country.
"But we warmly welcome the news that this will crucial work will be carried out. Linking our great northern cities is the first step to creating a stronger north: under-investment in transport connectivity means the North of England cannot behave as a single economy. Figures show there are 40% fewer commuter journeys between Leeds and Manchester than there should be, given their physical proximity.
"Now we would urge the Government to use the Spending Review and Control Period 6 to ensure the Northern Powerhouse can go full steam ahead. We need to see new cash, real money, spades in the ground on the range of projects put forward by northern leaders which can transform the region's prospects."
Anthony Smith, chief executive of independent watchdog Transport Focus, said: "Passengers will welcome the resumption of work to electrify the Midland Mainline and TransPennine routes. Electrification of a route can lead to faster journeys, and improved service frequency and punctuality."
Mick Cash, general secretary of the RMT rail union, said: "This politically motivated stop-start approach to crucial rail developments is no way to run a transport system and it is no surprise to us that this U-turn comes in the run-up to the Tory Party conference where RMT will be exposing the nonsense of the 'Northern Powerhouse' as part of the mass demonstration in Manchester on Sunday.
"This announcement does nothing to tackle the immediate threat to jobs, safety and services wrapped up in the new Northern and TPE franchises which RMT will continue to kick up the political agenda while George Osborne rattles on about his fantasy world light years off in the future."