The oldest surviving reference to Belcoo is in an Ulster saga called 'Argain Belcon Breifne,' or the Massacre of Belcu Brefne. The tale describes a trap set for the great Ulster hero Conall Cernach by a Breifne chief named Belcu. Conall managed to reverse the trap and caused Belcu's own sons to kill their father by mistake. The place where it happened was named for Belcu. A modern interpretation suggests instead that the name derives from words meaning 'mouth' and 'narrowing,' referring to the village's position on the narrow water-neck between the two loughs. The Book of Magauran from the 14th century calls it Cunga, the 1607 Inquisition at Dromahair mentions Beallacowngamore and Beallucowngabegg, and the 1609 Ulster Plantation map labels it Kiliconge, Coille Cunga, 'the wood of the narrow strip of land.' A more colourful derivation gives Beal Cu, 'the mouth of the hound,' and a Belcoo folktale recorded by Maire MacNeill in her 1962 book on the Festival of Lughnasa describes balefire coming out of a hound's mouth before the hound was killed by Saint Patrick.

During the Irish Rebellion of 1641, the English Army built a fort at Belcoo that appears on the Down Survey maps of 1655. When the Irish surrendered at Cavan on 27 April 1653, paragraph seven of the Articles of Surrender specifically required Colonel Hugh McGuire's regiment to lay down their arms at 'Belcowe fort, in the county of Fermanagh' by 18 May next. The fort was still functioning in 1700, when the Calendar of Treasury Books recorded an allowance of 14 pounds per annum for fire and candle for the barracks, with a single foot soldier in residence. Reverend William Henry, writing in 1739, described how 'Lough Macnane is contracted into a narrow, deep canal, in which form it flows through a flat meadow for half a mile to the redoubt of Bellcoe, where is a good ford and a new bridge across it.' The bridge that still spans the river divides the village in two, with the Republic of Ireland beginning on the far bank.

With the partition of Ireland in 1921, Belcoo became a border village. On 28 March 1922, during the turbulent post-truce period that would lead to the Irish Civil War, a column of fifty Irish Republican Army volunteers crossed from County Cavan and attacked the Royal Irish Constabulary barracks in Belcoo. The fight lasted three hours. Fifteen RIC officers were captured and marched back across the border, where they were held until 18 July. The Irish Boundary Commission in 1925 recommended that Belcoo, like several other Catholic border villages in Fermanagh, be transferred to the Irish Free State, but the recommendation was never enacted. Belcoo stayed in Northern Ireland. The border ran through the river, and would continue to run there throughout the Troubles, when the bridge between Belcoo and Blacklion was a permanent checkpoint and occasional flashpoint.

About two miles northeast of Belcoo, in the townland of Gardenhill, an old derelict homestead sits on a hillside off the side road to Boho. Parts of it possibly date from the early years of the Plantation of Ulster in the early seventeenth century. It was rented and later owned by the Hassard family for around three hundred years, a continuity unusual in this part of Ireland. Gardenhill is privately owned and not open to the public. A handful of other landscape features mark the deeper history: the Mullycovet corn mill, which functioned from 1830 until the 1920s, is being restored, and is one of the few surviving working mills of its era in Fermanagh. The Lough MacNean Tourism Initiative, in operation since 2003, has been working to draw visitors to a stretch of country that for decades was easier to think of in terms of its border tensions than its considerable beauty.

Saint Patrick's Holy Well, Dabhach Phadraig, still draws pilgrims annually as it has done for at least three centuries. The pilgrimage involves the traditional 'stations,' a series of prayers performed at specific points around the well. The site has been studied by folklorists and is documented in a long essay by Mairead O'Dolain in the Clogher Record, Volume 18, Number 1. The Sligo, Leitrim and Northern Counties Railway opened a station here in 1879 jointly serving Belcoo and Blacklion, hence the full name 'Belcoo and Blacklion.' The line closed on 1 October 1957, and the railway bridge across the river between the two villages was blown up by the British Army in the late 1970s to prevent its use by the IRA for moving arms across the border. The N16 from Sligo and the A4 from Enniskillen still meet here at the bridge, and crossing it today is a peaceful matter of changing currencies in your mental arithmetic, though for a long stretch of the twentieth century it was anything but.