Hundreds of trains were cancelled or delayed on Sunday amid staff shortages blamed on the World Cup and hot weather.
Great Western Railway (GWR), Northern and CrossCountry services were disrupted on Sunday as fewer train crews than normal agreed to work.
There was a chance that England could have been playing in the World Cup final at 4pm, until the team lost on Wednesday.
GWR issued a statement on Friday warning of disruption on Sunday because there would be a “significantly reduced number of available staff” due to factors including the World Cup final, the spell of warm weather and the start of the school holidays.
But a spokesman for the operator said on Sunday that more staff than expected have been available to work, meaning around 95% of services were running and 35 out of 850 were cancelled.
Full refunds are available for holders of Advance tickets, or passengers can use tickets on Monday instead.
Northern announced more than 170 services will be cancelled on Sunday.
The train operator said it is “likely” more services will be scrapped, with Cheshire, Lancashire and Greater Manchester faring the worst, and Yorkshire also affected.
A spokesman said “many Northern staff have made themselves unavailable for work” on Sunday.
Staff contracts mean they do not have to work Sundays if they provide seven days’ notice.
The Northern spokesman apologised and said: “Unfortunately we have so far had to cancel more than 170 services across our network and it is likely more will be cancelled as we continue to plan our services.”
CrossCountry trains were also disrupted due to a shortage of conductors.
Greater Manchester mayor Andy Burnham and his Liverpool counterpart Steve Rotheram recently criticised Northern for causing “extreme chaos” on networks for “far too long”.
Hundreds of services have been cancelled by the operator, Thameslink and Great Northern since departure schedules were modified on May 20.
Thameslink and Great Northern introduced a third new timetable in two months on Sunday.
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.
An interim timetable was introduced on June 4 which saw around 6% of daily services removed, but reliability continued to struggle.
Charles Horton, chief executive of Govia Thameslink Railway (GTR) – parent company of Thameslink and Great Northern – announced his resignation.