Commuters faced disruption in their train journeys due to a fault at Wigan Wallgate.
A problem with the signalling system meant services from the station were delayed, cancelled or re-routed on Monday morning.
Passengers heading into Manchester had to cross to Wigan North Western to get the train, while those travelling out of the city were also diverted to the other town centre station.
Services to Southport were also affected.
Northern said on social media the problem was solved by 9.20am.
Passengers delayed by 30 minutes or longer will be entitled to compensation. Find out more at northernrailway.co.uk/delayrepay