Travellers on Northern services on routes in Lancashire, Cumbria and Greater Manchester have suffered disruption for months due to delays to improve the line between Manchester and Blackpool, and hundreds of trains have been cancelled following the implementation of new timetables on May 20.
The region's transport body, Transport for the North (TfN), announced the framework of an initial package to compensate season ticket holders, agreed with the Department for Transport.
Weekly, monthly and annual pass holders who held tickets in the areas worst affected will receive a refund equivalent to the cost of four weeks' travel.
Season ticket holders in others areas affected since May 20 will receive a payment worth one week's travel.
The scheme will be implemented "rapidly", TfN said.
Proposals for compensation measures for passengers who do not hold season tickets are being developed.
TfN chairman John Cridland said: "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'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."
Meanwhile, a third new train timetable in two months will be introduced by Thameslink and Great Northern.
The latest change will still see some services cancelled in advance but rail bosses hope the number of on-the-day cancellations will be reduced.
Thameslink and Great Northern routes - part of the Govia Thameslink Railway (GTR) franchise - have suffered major disruption since May 20.
An interim timetable was introduced on June 4 which saw around 6% of daily services removed, but reliability has still struggled.
A GTR spokesman said: "We are very sorry for the continued disruption following the delayed approval of the new timetable.
"We are re-planning how we use trains and train crew on Thameslink and Great Northern to deliver a new fixed, interim timetable in July that will prioritise peak trains and reduce service gaps, progressively delivering improvement.
"We urge anyone delayed by 15 minutes or more to apply for compensation. This can be claimed against the original timetable and there is enhanced compensation for season ticket holders."
Crispin Blunt, Conservative MP for Reigate, Surrey, described his "acute exasperation" at the performance of services between London and Redhill.
"I am appalled at the operator's failure to address ongoing and severe service gaps and cancellations on local services," he said.
"These ongoing service failings are causing so much misery and hardship for my constituents and once again it seems the Redhill service is being sidelined despite the large numbers of passengers using it. This is completely unacceptable."
A series of failures have been blamed for causing the chaos, including Network Rail's late approval of the new timetables and delayed electrification projects, poor planning by train operators and the decision by transport ministers to phase in the introduction of new GTR services.