But the decision by Transport for the North to approve the measures was nearly delayed as northern leaders raised concerns about whether rail operator Northern ought to be footing the bill.
Under the scheme revealed at a meeting of TfN's board today, passengers with season tickets since April in the North West, which was worst hit by the disruption, will be able to claim compensation for four weeks of rail travel.
But after lobbying from politicians outside the North West, season ticket holders on Northern's West Yorkshire routes since the botched introduction of a timetable on May 20 and those on affected TransPennine Express services will be entitled to claim one week's worth of train travel back.
The decision was made in the final seconds of the strategic body's meeting at Manchester Town Hall, which members were told had to end at 12.45pm as another meeting was scheduled in the same room immediately afterwards.
A discussion had been set to be held in private about compensation for those affected, before objections by a number of northern leaders meant it was held in public.
And at one point it looked as if no agreement would be reached as concerns were raised by metro mayors Andy Burnham and Steve Rotheram that the package would be funded by the public body Network Rail and not operator Northern.
Rail Minister Jo Johnson, who was present for the meeting, said he was "deeply regretful" that leaders would be leaving the room without an agreement to announce.
In the end, it was agreed that the compensation would be approved for season ticket holders and a funding package agreed for marketing purposes for affected areas such as the Lake District and Blackpool
Transport for the North expects that the agreed compensation scheme "will be implemented rapidly" after being agreed by the Rail North partnership, which runs the Northern franchise.
This compensation is on top of the pre-existing 'delay repay scheme' and will also apply to season ticket holders who hold multi-modal travel tickets.
The issue of the level of compensation for passengers without season tickets who have suffered hardship as a result of the delays and cancellations is to be discussed further and decided at a later date.
During the meeting, TfN's independent chairman John Cridland described the Northern timetable chaos as a crisis and said the strategic body and Rail North, which manages the franchise, should look at its own performance.
He said in a statement after the meeting: “We know that the past few months have been very frustrating for many northerners, with those who regularly travel by train being heavily affected. The Transport for the North board has been pressing the rail industry to adequately compensate those who have suffered the most. I
"I’m delighted that we are now able to start doing this but there is still more work to be done.
“Compensation for season ticket holders will be administered directly by the train operating companies, with Northern and TransPennine Express due to announce details of how people can claim very soon.”
Speaking after the meeting, Cllr Judith Blake, Leader of Leeds City Council and West Yorkshire Combined Authority representative on the TfN Board, said: “Today’s decision ensures some compensation will begin to flow to rail passengers as soon as possible but it is clear that what was on offer can only be a starting point and that the rail industry must come forward with a more comprehensive package which properly compensates rail passengers across the North of England.
"We must also ensure the rail companies foot their rightful share of this bill. Rail passengers have had to endure weeks of chaos and they deserve proper compensation for the disruption to their lives and businesses.”