Train operator Northern Rail has been running a limited service on a handful of routes after staff walked out in a row over bank holiday pay.
The Rail Maritime and Transport (RMT) union said about 1,000 conductors were on strike from 0001 GMT on 27 December until midnight on 28 December.
It wants conductors to receive double pay for working on bank holidays.
Northern Rail said it was disappointed by the strike and ran a service from 0900 to 1800 GMT.
Many trains between Manchester, Liverpool, Preston, Leeds and Newcastle did not run.
Routes between Carlisle, Sheffield and York and out of Stoke have also been affected.
The company said about 25% of services were running to and from Hull and Bridlington in East Yorkshire and Cleethorpes in North East Lincolnshire.
The RMT said the pay for bank holidays had been agreed with the union several years ago after conductors traded double pay for other benefits including increased salaries and extra annual leave.
It argued that there was no agreement in place on Northern Rail for the additional public holidays on 27 and 28 December.
RMT regional official John MacDonald blamed Northern Rail for the walkout.
"This could have been solved so easily and Northern didn't have the will to solve it and that's what is so frustrating about today," he said.
"They met us on 22 November and we have had no contact since."
Ian Bevan, managing director of Northern Rail, said: "We are very disappointed that the RMT is going ahead with strike action when only 361 of 976 conductors voted for a strike.
"We have said all along that we will honour the existing agreements that we have with the trade union, and we are always willing to hold further talks.
"Our priority now is to ensure that our passengers have all the information they need to make an informed decision about their travel plans on 27 and 28 December."