The problems began early on Thursday when NIR's 06:15 BST service from Belfast to Newry broke down across a set of points at Central Station.
The position of the train meant that NIR could only operate one of its four platforms at Central Station.
The train has now been moved and services are returning to normal.
The rail junction had been blocked for several hours on Thursday morning.
A Translink spokeswoman said the knock-on delays had affected train services between Belfast and Newry, Bangor, Portadown, Larne and Londonderry.
The company apologised to its passengers and said it had been working hard to "keep delays to a minimum".
A broken down train that caused long rush-hour delays on all of Northern Ireland Railways' services is no longer blocking the line at a Belfast station.