Around a quarter of TransPennine Express (TpE) and Northern passengers unsuccessfully applied for compensation between April and October 2018.
TpE paid out in 74 per cent of cases, while Northern did in 77 per cent, both lower rates than average, a JPIMedia date investigation revealed.
However claims by 18,958 TpE passengers and 30,917 Northern passengers were thrown out.
Both operators trailed behind London North Eastern Railway, which operates the London Kings Cross to Leeds service, which paid out on 85 per cent of claims.
Another Yorkshire operator, Grand Central, however, awarded compensation in just 58 per cent of the cases.
Passenger groups say many compensation schemes remain too complicated and time-consuming and they would like to see a simple set of rules and processes across all train operators.
Only a third of passengers eligible for compensation actually claim it, according to Transport Focus.
Rod Tickner, of the Aire Valley Rail Users’ Group, said many commuters had “become resigned to the sort of service they get” and going through the claims process was just another “piece of hassle.” He added: “I think an awful lot of people shrug their shoulders and say it’s the railways.”
The best performing operator in the country Merseyrail paid out in 100 per cent of the cases.
Northern Powerhouse Partnership Director Henri Murison said: "In the context of the Williams Rail review, which is focussed on customers who use and rely on the railway, these figures make interesting reading.
"The highest pay out rates are upheld by Mersey Rail, which works for local government in the Liverpool City Region rather than answers to the Treasury and Department for Transport.
"LNER, about to start introducing their new Azuma trains between Leeds and London, has a much higher acceptance of claims than Grand Central, an open access operator who are not required to invest in the services available on the East Coast mainline in the same way - not contributing to improving wifi for example."
Stephen Waring, chair of Halifax & District Rail Action, said there was a further problem in West Yorkshire with train companies not paying compensation on multi-modal travel cards, like the MCard. He said: “A high proportion of Leeds commuters will use MCards.
“Surely if their train is late they should be entitled to compensation just as they would if they had a rail-only ticket.”
The Government says it is working to roll out its preferred compensation scheme, Delay Repay 15, which pays for delays over 15 minutes, across all operators and introducing speedy "one click" compensation on future franchises.
Northern’s figures exclude the enhanced compensation scheme following the May timetable chaos.
AUTOMATIC REFUNDS are on the way for TransPennine Express passengers
Currently TpE offers the standard Delay Repay 30 compensation scheme, which means passengers can claim half their ticket price back for delays of 30 minutes and a full refund for delays of an hour or more.
A spokeswoman for TpE said they advertised Delay Repay via announcement, posters and their website and said they were working on details of an automated repayment system, which will go live later this year.
Since December Northern, has been running a Delay Repay 15 system, which also pays back a quarter of the rail fares for delays of 15 to 30 minutes.
In a statement, the operator said every valid Delay Repay claim was “paid quickly and efficiently with a negligible number of rejections.”
It added: “Customer awareness of Delay Repay and propensity to claim is evident in the fact that since the peak of claims caused by the May timetable last year, the volume of claims has reduced in line with performance improvements but remains twice at the level of before.”
Rail operators say their efforts to encourage more people to claim has seen compensation payouts increase to £81m a year, an 80 per cent rise in two years.
How did your rail operator fare?
Rail operator Number of compensation claims decided on Number of claims approved Percentage of successful claims (April 1 to October 13, 2018)
Grand Central 7,087 4,132 58 per cent
TransPennine Express 73,778 54,820 74 per cent
Northern 132,246 101,329 77 per cent
Hull Trains 2,619 2,381 83 per cent
London North Eastern Railway 260,391 220,669 85 per cent
*Hull Trains did not submit figures for April 1 to June 23, 2018