The 1998–99 North West Counties Football League season was the 17th in the history of the North West Counties Football League, a football competition in England.
Teams were divided into two divisions: Division One and Division Two.
Division One featured five new teams: Division Two featured five new teams: Vauxhall GM beat Prescot Cables 1–0 in the final in a replay after the original match finished 1–1.
Clitheroe beat Kidsgrove Athletic 2–1 in the final.
Fleetwood Freeport beat Warrington Town 2–1 in the final.