Rail services running into Wigan were disrupted following a points failure elsewhere on the network.
Passengers taking Northern services into Wigan Wallgate from Southport, a line which runs through Parbold, Appley Bridge and Gathurst, facing travel difficulties for much of Thursday.
The problems began during the early-morning rush hour and were not completely fixed until around 2.30pm.
Northern admitted on social media services were cancelled or delayed by up to 45 minutes.
The problem actually occurred somewhere between Manchester Piccadilly and Newton-le-Willows but the knock-on effect was felt all over the region's network.