A combination of the increasing road competition facing all railways and a change in patterns of economic activity caused by the partition reduced the GNRI's prosperity. The company modernised and reduced its costs by introducing modern diesel multiple units on an increasing number of services in the 1940s and 1950s and by making Dublin–Belfast expresses non-stop from 1947. In Dundalk at the GNRI works, the railway engineers developed railbuses for use on sections of the rural network.
Nevertheless, by 1947 the GNRI had ceased to be profitable and in late 1950, the situation had become so bad that the company's shareholders authorised the board to close the entire railway. This forced the Irish and Northern Irish governments into action and they soon started negotiating a buy-out. An agreement was reached for a purchase price of £4.5 million (split evenly between the two governments) as well as the financing of all debt incurred before the deal was finalised. This happened on 1 September 1953 after the passage of legislation in both jurisdictions. The new entity was named the Great Northern Railway Board (GNRB) and was run jointly, with half of the board's 10 members appointed by each government.
The new Board's main task was to improve the finances of the railway. The first step was to replace the outdated and worn-out rolling stock. An order for railcars was soon placed, however an order for diesel locomotives was never sanctioned by the governments, leading to increasing frustration from the Board as the matter dragged out. A railcar maintenance depot was opened in Fairview in 1958 to service the new fleet.
The other key step was to close uneconomic lines, so on 1 May 1955 all services were ended on the Scarva–Banbridge, Banbridge–Castlewellen and Goraghwood–Markethill lines. Additionally, passenger services were ended on the Cookstown branch on 16 January 1956 and on 30 April of the same year, the Knockmore Junction–Banbridge line was closed.
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More widespread closures were proposed unilaterally by the Northern Ireland minister of commerce, Daniel Dixson in 1956. He wanted three lines to be closed on the Northern Ireland side up to the frontier: Omagh–Newtownbutler (including the Fintona horse tram), Portadown–Tynan and Bundoran Junction–Belleek. Not only were these closures not supported by his southern counterpart or the Board, but they would have also forced closures on the other side of the border, as the remaining stubs of lines would no longer be viable. In response to these plans, statutory tribunals were held in each jurisdiction. The evidence given by stakeholders was overwhelmingly against the closures, and notably Dixson did not given any evidence, nor did anyone present his views on his behalf. The two tribunals had completely different findings. The southern one recommended that the lines remain open, while the northern one said they should be closed. The Northern Ireland government felt the matter decided, and so the lines were closed on 30 September 1957. Within a few weeks, passenger services on the corresponding lines on the other side of the border had also ceased (Dundalk–Clones, Cavan–Glaslough and the Belturbet branch). In all, almost 200 miles (320 km) of railway had been decimated, leaving large areas of the county without access to trains.
In June 1957, Dixson announced he intended to end the joint ownership arrangement and it was agreed that the organisation would be split and merged into the two jurisdictions' nationalised transport companies: The Ulster Transport Authority (UTA) and Córas Iompair Éireann (CIÉ). One of the final acts of the company was to end passenger services on the Oldcastle branch on 12 April 1958. On 1 October, the railways lines were split at the border and all other assets were divided, with the exception of Dundalk works, which was spun off as its own company. The entity itself remained as a holding company for the County Donegal Railways Joint Committee as it had half-ownership of it and could not be dissolved until that company's winding up had been completed. This finally happened in 1981. All classes of locomotive and rolling stock were divided equally between the two new owners. Most classes of GNRI locomotive had been built in small classes, so this division left both railways with an operational and maintenance difficulty of many different designs all in small numbers.
After the split, further closures were carried out and today the only remaining lines of the former company are Belfast–Dublin, the Howth Branch, Drogheda–Navan and Lisburn–Antrim, of which only the first two have passenger services.