But trains on routes between Preston, Wigan, Kirkby, Gathurst and Warrington are likely to be impacted for the rest of the day, with disruption to Avanti West Coast, Northern and TransPennine Express services.
Journeys on the network are likely to be disrupted until 4pm, said Network Rail, and bus replacements are running between Preston, Wigan North Western, Warrington Bank Quay and Crewe.
Network Rail said journey times will be extended by up to 2 hours when using road replacement transport.
It added that passengers travelling between Blackpool / Preston and Liverpool can use any available Northern service via Manchester stations.
A spokesman for Network Rail said: "The fault with the signaling system in the Wigan North Western area has now been fixed and services are beginning to return to normal at this station.
"However, trains may still be cancelled, delayed by up to 70 minutes or revised. This is expected until 4pm.
The railway operator is urging people to check www.nationalrail.co.uk or with their individual train operator for the latest travel information.
Chris Pye, Network Rail’s North West route infrastructure director, said: "I’m extremely sorry we have been unable to give passengers the service they expect and deserve today.
"My teams have now fixed the complex fault but it will take some time to get trains back to the normal timetable again.
"I’d like thank all those people delayed for their continued patience and I’d urge anyone planning to travel today to check National Rail Enquiries for the latest travel information."