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".

The authority has reduced the frequency of grass cutting to save money.
But it has led to complaints from residents, with the overgrowth said to be "destroying" people's final resting places.
The council said it has brought forward its next scheduled cut in many locations.
Councillor Dilwyn Lloyd has received complaints about a park in his ward of Talysarn. He said the long grass posed a risk to the public.
Meanwhile, Nerys Owen-Jones recently visited her mother's grave at Coetmor cemetery in Bethesda and was "deeply saddened" by what she saw.
"I drove up to my mum who thankfully has my father maintaining her plot, but apart from a few others, it's all overgrown," she said.
"There are a few there that I know will never be looked after as there are no children and the wives/husbands are not capable.
"It's so very sad that your last resting place ends up under council cutbacks and the visiting place for families is destroyed."
She added: "The grass cutting service needs to be reinstated immediately. It's a disgrace."
In March Gwynedd council approved a programme of service cuts totalling Â£4.94m. It included an option to reduce the frequency of grass cutting.
A council spokesman said: "It must unfortunately be accepted that less frequent grass cutting will inevitably lead to a deterioration in the tidiness of some areas during certain times of the year.
"However, the very recent spate of growth means that the council has brought forward the next scheduled cut in may locations throughout the county, and this work is being carried out as quickly as possible."

Police said there was "an altercation" between a motorcyclist and a car driver after the collision in North Wingfield Road, in Grassmoor, Chesterfield, at about 21:00 BST on Tuesday.
The 74 year-old man, who was driving the car, died in hospital. The biker is in police custody being questioned.
A murder investigation is under way into the death.
Det Ch Insp Gareth Meadows, who is leading the investigation, has asked anyone who witnessed the crash outside the Boot and Shoe Inn to contact the force.
More on this and other stories from across the East Midlands
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.
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Gwynedd council has been criticised for not cutting the grass in its cemeteries, play areas and open spaces.
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A 30-year-old man has been arrested on suspicion of murder following an argument after a crash in Derbyshire.