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
Division One featured five new teams:
Bootle, promoted as seventh place in Division Two
Cheadle Town, promoted as fourth place in Division Two
Leek CSOB, promoted as third place in Division Two
Skelmersdale United, promoted as runners-up of Division Two
Workington, relegated from the NPL Division One
League table
Division Two
Division Two featured five new teams:
Abbey Hey, joined from the Manchester League
Chadderton, relegated from Division One
Curzon Ashton, transferred from the Northern Counties East Football League
Darwen, relegated from Division One
Warrington Town, relegated from Division One
League table
Cup competitions
League Challenge Cup
Vauxhall GM beat Prescot Cables 1–0 in the final in a replay after the original match finished 1–1.
Floodlit Trophy
Clitheroe beat Kidsgrove Athletic 2–1 in the final.
Division Two Cup
Fleetwood Freeport beat Warrington Town 2–1 in the final.