The first election to Fermanagh County Council took place in April 1899 as part of that year's Irish local elections.
The election saw the council split evenly between Unionists and Nationalists. Concurrent district council elections saw Nationalists and Unionists both win 33 seats for Enniskillen Rural Council. Nationalists won a large majority on Enniskillen Board of Guardians, as 8 Cavan Divisions (which all returned Nationalists) were joined to the union. Nationalists won a majority on Lisnaskea Guardians and District Council, while Unionists won control of Irvinestown Council.