Photos showed hundreds of passengers packed inside King's Cross and Paddington, with some journeys delayed due to the late handover of engineering works.
In Scotland, some ScotRail services started running again from 7:15am, but many routes did not return to normal until later in the day.
Travel journalist Simon Calder said there was "chaos" at Paddington, with no trains having arrived or departed by 10am despite industrial action by the RMT union ending at 6am.
A Network Rail spokesperson said: "Services have been generally OK, but we did have some disruption this morning at Paddington because of the late handover of some engineering works."
It comes after passengers were told to prepare for "significantly disrupted" travel into the new year amid the wave of industrial unrest sweeping across the country.
The RMT intends to hold a further four days of strike action next week amid its UK-wide dispute, with the industrial action meaning ScotRail will only run a limited service between January 3 and 7.
Liam Sumpter, route director for Network Rail Scotland, apologised to passengers in a statement published by the BBC.
He said: "We remain committed to working with the RMT to find a solution to this dispute, but we also need to agree a deal that is fair on the taxpayers who fund our railway."
The Network Rail warning came as members of the Transport Salaried Staffs' Association (TSSA) at CrossCountry staged a 24-hour strike from 9pm on Boxing Day as part of a long-running campaign for a guarantee of no compulsory redundancies, no unagreed changes to terms and conditions, and a pay increase which addresses the rising cost of living.
The 48-hour walkout called by the RMT in a separate dispute over jobs, pay and conditions, which began on Christmas Eve ended at 6am, but disruption has continued.
The TSSA union said it believed walkouts by staff would severely affect services at CrossCountry, which covers large swathes of the country, from Penzance to the Midlands, Wales and northern England through to Scottish cities as far north as Aberdeen.
TSSA members work in roles in customer service management, driver management, training, control, customer communications, safety, timetabling and planning.
Earlier TSSA organising director Nadine Rae said: "Our members at CrossCountry do not want to strike, especially over the Christmas holiday period, but they are sick and tired of being taken for granted.
"They deserve a pay rise to help manage the escalating cost of living, and they rightly demand job security.
"The company, like all the train operators under the control of the Department for Transport, need to face up to the fact that only serious offers which meet our aspirations will end this dispute."
A Department for Transport spokesman said: "After two years of virtual Christmases, the British public deserve better than to have their festive celebrations impacted by strikes.
"The transport secretary and rail minister have worked hard to facilitate a fair and reasonable offer, which two unions have accepted, and it is incredibly disappointing that some continue to strike.
"We urge them to step back, reconsider and get back round the table, so we can start 2023 by ending this damaging dispute."