Wigan North Western station was cleared shortly after 08:40 GMT after part of the archway fell on to parked cars.
Northern and Arriva North West rail companies said there could be severe delays for some time.
Greater Manchester Police said no injuries had been reported and the station would remain closed until further notice.
The A49 Queen Street, Wallgate, Great George Street and King Street West have all been closed to traffic.
A diversion for traffic heading into the town centre has been put in place off Saddle junction on to Warrington Road and Poolstock Lane, Wigan Council said.
The collapse caused travel problems across the region, with delays to Northern and Virgin trains.
Virgin Trains tweeted all lines had since reopened with speed restrictions.
A spokesman for Network Rail said the collapsed structure was "part of a disused subway, which runs underneath the railway and above the road, [and has] long been blocked off and filled in".
He added that the problem was affecting platform six, which remains closed, and a "full assessment of the structure will take place to inform any repair work".
A railway arch has partially collapsed in Wigan, causing the evacuation of a station and delays to train services.