Passengers who travel with TransPennine Express could be in line for partial refunds for the "unacceptable" services at the back end of 2019.
A new timetable was brought in during December, but it was fraught with delays and cancellations, leaving thousands of passengers stranded.
In fact, it has become so bad that the on the Liverpool to Edinburgh route - which includes trains through Leeds - because the roll-out of a new fleet is taking longer than expected.
The company's managing director Leo Goodwin has admitted that the December debacle was "not up to scratch" and has offered season ticket holders a three per cent rebate.
It applies to all season ticket holders between October 1 and December 31, 2019 and is slightly more than the 2.8 per cent increase in fares which came into effect this month.
'It is only right that we compensate our customers for the recent disruption'
Mr Goodwin said: "We know that our performance was not up to scratch at the end of last year and for this we really do apologise.
"We have experienced a number of issues following the introduction of our new trains, resulting in disruption to a number of our customers journeys with us.
"I would like to thank our customers for continuing to travel with us and it is only right that we compensate them for the recent disruption."
However, 17 of the operator’s services from Newcastle, Durham and Darlington that call at York, Leeds, Manchester and Liverpool will continue to be out of action until January 24.
The compensation scheme will go live on Monday, January 13 until Saturday, February 29, and can be claimed in addition to delay repay, which entitles all season and non-season ticket holders to receive a refund for journeys delayed for 30 minutes or more.
More information is available on the TransPennine Express website .
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