The SL&NCR opened as far as Belcoo in 1879, Manorhamilton in 1880, Collooney in 1881 and Carrignagat Junction on the Midland Great Western Railway (MGWR) opened in 1882,The SL&NCR opened as far as Belcoo in 1879, Manorhamilton in 1880, Collooney in 1881 and Carrignagat Junction on the Midland Great Western Railway (MGWR) opened in 1882, completing a line of about 43 miles (69 km). Beyond Carrignagat Junction the SL&NCR exercised running powers over the MGWR to and from Sligo.
In 1895 the Waterford, Limerick and Western Railway (WL&WR) was extended to Collooney, forming junctions with the MGWR and SL&NCR. This gave access to a larger area of western Ireland, whose cattle exports formed a significant part of the SL&NCR's traffic.
In 1878 a stationmaster’s house and six houses were built for SL&NCR workers and their families at Belcoo, County Fermanagh. Belcoo station opened in 1879, serving both Belcoo and Blacklion, County Cavan. The last trains through the station ran on 20 September 1957.
The SL&NCR was one of the railways that the Irish Free State's Great Southern Railways did not absorb in 1925 because it crossed the border with Northern Ireland. It became the last privately owned railway undertaking to survive in Ireland (although the Londonderry and Lough Swilly Railway still existed as a road transport firm).
The company never prospered since the countryside it crossed was poor and sparsely populated, although at one time intermittent heavy cattle traffic used the line. Governments on both sides of the border subsidised the railway in its later years, but the SL&NCR closed on 1 October 1957 as a result of the Government of Northern Ireland making the GNR Board close its line through Enniskillen.
SL&NCR locomotives had names, but were not numbered. The company had the use of only two turntables: its own at Enniskillen and the Midland Great Western Railway one at Sligo, and so tank engines were the preferred option.
In 1904 Beyer, Peacock delivered Sir Henry, an enlarged and modernised 0-6-4T design, the SLNCR Sir Henry class. Enniskillen was delivered in 1905 and "Lough Gill" in 1917. All three survived until the closure of the line in 1957.
The SL&NCR was an early adopter of railbusesrailbuses and railcars, which it introduced in the 1930s and 1940s. One of the latter, Railcar B, was built in 1947 and is now preserved by the Downpatrick and County Down Railway at Downpatrick.