The improvements between Preston and Manchester, including electrification, have been delayed by around two years but Network Rail will now begin the final phase of its work.
This will involve a full closure between Saturday, August 25, and Sunday, September 2, with replacement buses running from Bolton instead of trains.
Engineers have also announced an end-date of Sunday, November 4, for mid-week overnight works and weekend works on lines through Bolton.
Martin Frobisher, managing director for Network Rail’s London and North Western route, said he was sorry for the "short-term disruption" caused by these plans, but urged passengers to focus on the eventual advantages provided by the work.
He said: “Our Manchester-Preston upgrade is part of the Great North Rail Project, the rail industry’s team effort to transform train travel for customers across the North through track and train improvements.
“I’m sorry for the further short-term disruption that this work will cause, but please don’t lose sight of the long-term improvements which will be delivered.
"In future electric-powered, greener, faster, more frequent, more spacious, more reliable trains will become the norm through the Bolton corridor.”
In May, trains out of Bolton were hit with a raft of delays and cancellations caused after last-minute edits to the national timetable change created a lack of drivers.
Northern managing director David Brown laid the blame for some of this at the feet of government-managed Network Rail.
In an interview with The Bolton News in July, he said: “It’s really clear that, the root cause is two things, but one is that we were trying to run a timetable based on a set of infrastructure works - electrification to Blackpool and the Bolton corridor - that’s been either heavily delayed or just delayed and that has then led to us rewriting the timetable in a really short space of time, three months rather than nine or 10 months."
Mr Frobisher addressed this issue when he announced the changes, he said: “We recognise the May timetable change resulted in poorer service for many customers than it should have done.
"We are working together with our train company partners to resolve current issues as soon as possible.”
The delays to Network Rail's programme of works have been partially attributed to the failure of construction giant Carillion, which was used as the primary contractor for the project until it fell into liquidation in January.
The firm was Network Rail's second largest maintenance service supplier and was heavily involved in the HS2 project, as well as electrification.
Infrastructure company Amey has now been appointed as the main contractor for the Preston-Manchester upgrade, meaning the programme of work should be progressing to schedule again.
The work has included the remodelling of the Farnworth Tunnel at Moses Gate and the renewal of nearly 14km of track.